PDB Short entry for 1MUW HEADER ISOMERASE 24-SEP-02 1MUW TITLE THE 0.86 ANGSTROM STRUCTURE OF XYLOSE ISOMERASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 EC: 5.3.1.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES OLIVOCHROMOGENES; SOURCE 3 ORGANISM_TAXID: 1963; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HB101; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PX15 KEYWDS XYLOSE ISOMERASE, ATOMIC RESOLUTION, DISORDER, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.D.FENN,D.RINGE,G.A.PETSKO REVDAT 5 14-FEB-24 1MUW 1 REMARK LINK REVDAT 4 24-JUL-19 1MUW 1 REMARK REVDAT 3 13-JUL-11 1MUW 1 VERSN REVDAT 2 24-FEB-09 1MUW 1 VERSN REVDAT 1 06-NOV-02 1MUW 0 JRNL AUTH T.D.FENN,D.RINGE,G.A.PETSKO JRNL TITL ACTIVE SITE DYNAMICS AT 0.86A: CRYSTALLOGRAPHIC ANALYSIS OF JRNL TITL 2 A METAL-MEDIATED HYDRIDE SHIFT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.86 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.126 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.125 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 3.700 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 17954 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 358727 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.099 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.099 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.116 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 12674 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 254736 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3025 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 449 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3477.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2913.3 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 88 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 35246 REMARK 3 NUMBER OF RESTRAINTS : 49011 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 ANGLE DISTANCES (A) : 0.033 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.102 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.095 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.046 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.116 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1MUW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-OCT-02. REMARK 100 THE DEPOSITION ID IS D_1000017202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI-111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 358727 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.40 REMARK 200 R MERGE FOR SHELL (I) : 0.56500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: PDB ENTRY 1XYA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.97 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10MM MGCL2, 2.2M (NH4)2SO4, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 42.95300 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.44150 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.16050 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.95300 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.44150 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.16050 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.95300 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.44150 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.16050 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.95300 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.44150 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.16050 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 32330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -267.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 92.88300 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 92.88300 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 593 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 713 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 862 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 872 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 899 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HH22 ARG A 373 O HOH A 774 0.46 REMARK 500 NH2 ARG A 9 NH1 ARG A 283 0.76 REMARK 500 HA SER A 1 O HOH A 746 1.00 REMARK 500 OE2 GLU A 159 O HOH A 537 1.11 REMARK 500 HD2 HIS A 95 H VAL A 97 1.12 REMARK 500 NH2 ARG A 373 O HOH A 774 1.13 REMARK 500 HG22 THR A 84 O HOH A 854 1.25 REMARK 500 H ASP A 174 O HOH A 875 1.37 REMARK 500 HE ARG A 156 OE1 GLU A 159 1.41 REMARK 500 HH22 ARG A 9 NH1 ARG A 283 1.42 REMARK 500 HH21 ARG A 9 NH1 ARG A 283 1.42 REMARK 500 NH2 ARG A 9 HH11 ARG A 283 1.42 REMARK 500 NH2 ARG A 9 HH12 ARG A 283 1.42 REMARK 500 HD2 HIS A 48 O HOH A 853 1.44 REMARK 500 HH12 ARG A 204 O HOH A 877 1.47 REMARK 500 HE22 GLN A 326 O HOH A 785 1.50 REMARK 500 HH21 ARG A 41 OE1 GLU A 44 1.50 REMARK 500 HD3 ARG A 67 O HOH A 842 1.53 REMARK 500 HH21 ARG A 156 OE2 GLU A 159 1.55 REMARK 500 HH12 ARG A 204 O HOH A 819 1.59 REMARK 500 H ASP A 174 O HOH A 875 1.60 REMARK 500 HH11 ARG A 67 O HOH A 630 1.60 REMARK 500 OE2 GLU A 324 O HOH A 774 1.74 REMARK 500 N ASP A 174 O HOH A 875 1.81 REMARK 500 CA SER A 1 O HOH A 746 1.81 REMARK 500 OD1 ASP A 344 O HOH A 860 1.82 REMARK 500 NH1 ARG A 204 O HOH A 819 1.84 REMARK 500 NH2 ARG A 9 CZ ARG A 283 1.86 REMARK 500 O HOH A 760 O HOH A 863 1.92 REMARK 500 CD GLU A 159 O HOH A 537 1.96 REMARK 500 OE2 GLU A 348 O HOH A 831 1.99 REMARK 500 CD2 HIS A 48 O HOH A 853 1.99 REMARK 500 CG2 THR A 84 O HOH A 854 2.02 REMARK 500 CZ ARG A 373 O HOH A 774 2.06 REMARK 500 OD2 ASP A 256 O HOH A 879 2.07 REMARK 500 CZ ARG A 9 NH1 ARG A 283 2.09 REMARK 500 O HOH A 742 O HOH A 876 2.09 REMARK 500 O HOH A 733 O HOH A 847 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 HD2 ARG A 265 O HOH A 715 2565 1.50 REMARK 500 O HOH A 716 O HOH A 716 3655 1.85 REMARK 500 CD ARG A 265 O HOH A 715 2565 1.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ARG A 315 NE ARG A 315 CZ -0.106 REMARK 500 ARG A 315 CZ ARG A 315 NH2 0.097 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 2 C - N - CA ANGL. DEV. = 18.3 DEGREES REMARK 500 TYR A 2 N - CA - CB ANGL. DEV. = 12.5 DEGREES REMARK 500 ARG A 9 NH1 - CZ - NH2 ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -14.4 DEGREES REMARK 500 ARG A 22 NH1 - CZ - NH2 ANGL. DEV. = 7.8 DEGREES REMARK 500 ARG A 22 NE - CZ - NH1 ANGL. DEV. = -5.1 DEGREES REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 73 CD - NE - CZ ANGL. DEV. = 38.6 DEGREES REMARK 500 ARG A 73 NH1 - CZ - NH2 ANGL. DEV. = 11.0 DEGREES REMARK 500 ARG A 73 NE - CZ - NH1 ANGL. DEV. = 6.5 DEGREES REMARK 500 ARG A 73 NE - CZ - NH2 ANGL. DEV. = -17.5 DEGREES REMARK 500 ARG A 75 NE - CZ - NH1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 GLN A 76 CA - CB - CG ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG A 108 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 120 NH1 - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = -8.8 DEGREES REMARK 500 ARG A 151 CD - NE - CZ ANGL. DEV. = 16.4 DEGREES REMARK 500 ARG A 151 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 TYR A 173 CB - CG - CD1 ANGL. DEV. = 5.3 DEGREES REMARK 500 TYR A 173 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 TYR A 173 CG - CD2 - CE2 ANGL. DEV. = 5.2 DEGREES REMARK 500 ASP A 174 N - CA - CB ANGL. DEV. = 11.6 DEGREES REMARK 500 ASP A 174 CB - CG - OD1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ASP A 174 CB - CG - OD1 ANGL. DEV. = 9.2 DEGREES REMARK 500 ASP A 174 CB - CG - OD2 ANGL. DEV. = 8.7 DEGREES REMARK 500 ASP A 174 CB - CG - OD2 ANGL. DEV. = -9.5 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = -7.1 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 204 NE - CZ - NH2 ANGL. DEV. = -6.2 DEGREES REMARK 500 TYR A 211 CB - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TYR A 253 CB - CG - CD1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 283 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 GLU A 336 N - CA - CB ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG A 353 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 PHE A 356 CB - CG - CD1 ANGL. DEV. = -4.4 DEGREES REMARK 500 GLU A 357 OE1 - CD - OE2 ANGL. DEV. = -11.6 DEGREES REMARK 500 ARG A 367 CD - NE - CZ ANGL. DEV. = 21.8 DEGREES REMARK 500 ARG A 367 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 367 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 373 CD - NE - CZ ANGL. DEV. = 15.0 DEGREES REMARK 500 ARG A 373 NE - CZ - NH1 ANGL. DEV. = -5.4 DEGREES REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 386 CB - CA - C ANGL. DEV. = 12.9 DEGREES REMARK 500 ARG A 386 NH1 - CZ - NH2 ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG A 386 NE - CZ - NH1 ANGL. DEV. = -6.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 52 ANGLE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 THR A 16 -77.24 -84.72 REMARK 500 PHE A 93 -29.39 -140.20 REMARK 500 GLU A 185 102.14 82.28 REMARK 500 ASN A 246 -168.57 -170.26 REMARK 500 SER A 249 48.78 -97.72 REMARK 500 SER A 249 55.91 -104.48 REMARK 500 TYR A 253 156.52 -47.15 REMARK 500 ALA A 342 60.71 -153.25 REMARK 500 PHE A 356 -77.30 -155.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER A 1 TYR A 2 -59.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 454 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 57 O REMARK 620 2 HIS A 70 ND1 86.8 REMARK 620 3 HOH A 539 O 114.7 101.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 453 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 OD1 REMARK 620 2 ARG A 207 N 108.8 REMARK 620 3 ARG A 207 N 108.1 0.7 REMARK 620 4 TYR A 211 OH 111.4 132.0 132.5 REMARK 620 5 HOH A 829 O 106.3 101.8 102.3 91.1 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 452 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 180 OE2 REMARK 620 2 GLU A 180 OE2 13.2 REMARK 620 3 GLU A 216 OE1 98.2 101.3 REMARK 620 4 ASP A 244 OD2 110.3 99.1 129.2 REMARK 620 5 ASP A 286 OD2 121.1 132.7 95.1 104.0 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 451 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 216 OE2 REMARK 620 2 HIS A 219 NE2 83.6 REMARK 620 3 ASP A 254 OD2 163.7 95.8 REMARK 620 4 ASP A 254 OD1 103.7 95.2 60.1 REMARK 620 5 ASP A 256 OD1 85.0 167.9 94.0 83.5 REMARK 620 6 OH A 455 O 101.2 98.0 95.1 152.9 88.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 451 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 216 OE1 REMARK 620 2 GLU A 216 OE2 44.8 REMARK 620 3 HIS A 219 NE2 66.1 64.3 REMARK 620 4 ASP A 254 OD2 129.5 111.3 63.5 REMARK 620 5 ASP A 254 OD1 133.1 89.2 88.3 48.8 REMARK 620 6 ASP A 256 OD1 122.8 101.9 151.7 103.5 66.0 REMARK 620 7 ASP A 256 OD2 143.4 148.0 143.6 83.1 79.1 46.1 REMARK 620 8 OH A 455 O 68.0 112.4 86.2 105.3 152.4 122.1 89.4 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 451 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 216 OE1 REMARK 620 2 GLU A 216 OE2 46.5 REMARK 620 3 HIS A 219 NE2 86.9 83.5 REMARK 620 4 OH A 455 O 71.6 96.2 149.4 REMARK 620 5 HOH A 589 O 133.5 174.8 91.3 88.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 451 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 452 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 453 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 454 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OH A 455 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XYA RELATED DB: PDB REMARK 900 X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE ISOMERASE-SUBSTRATE REMARK 900 COMPLEXES POSITION THE SUBSTRATE AND PROVIDE EVIDENCE FOR METAL REMARK 900 MOVEMENT DURING CATALYSIS REMARK 999 REMARK 999 SEQUENCE AUTHOR STATES THE SEQRES IS NOT AVAILABLE IN THE REMARK 999 DATABASE, AS IT WAS NEVER DEPOSITED BY THE AUTHORS AT THE TIME. REMARK 999 THE REFERENCE TO THE CORRECTED SEQUENCE IS GERHARDT, E. (1993) REMARK 999 GEZIELTE MUTAGENESE EINES HISTIDINRESTES IM AKTIVEN ZENTRUM DER REMARK 999 D-XYLOSE ISOMERASE VON STREPTOMYCES OLIVOCHROMOGENES: REMARK 999 BIOCHEMISCHE UND STRUKTURELLE ANALYSE DER MUTANTE. PH.D. REMARK 999 DISSERTATION, UNIVERSITY OF HEIDELBERG DBREF 1MUW A 1 386 UNP P15587 XYLA_STROL 1 386 SEQADV 1MUW ILE A 175 UNP P15587 THR 175 SEE REMARK 999 SEQRES 1 A 386 SER TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY SEQRES 2 A 386 LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY SEQRES 3 A 386 ASP ALA THR ARG PRO ALA LEU ASP PRO VAL GLU THR VAL SEQRES 4 A 386 GLN ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE SEQRES 5 A 386 HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP THR SEQRES 6 A 386 GLU ARG GLU SER HIS ILE LYS ARG PHE ARG GLN ALA LEU SEQRES 7 A 386 ASP ALA THR GLY MET THR VAL PRO MET ALA THR THR ASN SEQRES 8 A 386 LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR SEQRES 9 A 386 ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS SEQRES 10 A 386 THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA SEQRES 11 A 386 LYS THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SEQRES 12 A 386 SER GLY ALA ALA LYS ASP VAL ARG VAL ALA LEU ASP ARG SEQRES 13 A 386 MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SEQRES 14 A 386 SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO LYS SEQRES 15 A 386 PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL SEQRES 16 A 386 GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO SEQRES 17 A 386 GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN SEQRES 18 A 386 MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA SEQRES 19 A 386 LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY SEQRES 20 A 386 GLN SER GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY SEQRES 21 A 386 ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU SEQRES 22 A 386 LEU GLU SER ALA GLY TYR GLU GLY PRO ARG HIS PHE ASP SEQRES 23 A 386 PHE LYS PRO PRO ARG THR GLU ASP ILE ASP GLY VAL TRP SEQRES 24 A 386 ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU SEQRES 25 A 386 LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL SEQRES 26 A 386 GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA SEQRES 27 A 386 GLN PRO THR ALA ALA ASP GLY VAL GLN GLU LEU LEU ALA SEQRES 28 A 386 ASP ARG THR ALA PHE GLU ASP PHE ASP VAL ASP ALA ALA SEQRES 29 A 386 ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU SEQRES 30 A 386 ALA MET ASP HIS LEU LEU GLY ALA ARG HET MN A 451 3 HET MN A 452 1 HET MG A 453 1 HET MG A 454 1 HET OH A 455 2 HETNAM MN MANGANESE (II) ION HETNAM MG MAGNESIUM ION HETNAM OH HYDROXIDE ION FORMUL 2 MN 2(MN 2+) FORMUL 4 MG 2(MG 2+) FORMUL 6 OH H O 1- FORMUL 7 HOH *449(H2 O) HELIX 1 1 THR A 5 ASP A 8 5 4 HELIX 2 2 LEU A 14 GLY A 18 1 5 HELIX 3 3 ASP A 34 GLY A 46 1 13 HELIX 4 4 ASP A 54 ILE A 58 1 5 HELIX 5 5 SER A 63 GLY A 82 1 20 HELIX 6 6 HIS A 95 LYS A 99 5 5 HELIX 7 7 ASP A 107 GLY A 129 1 23 HELIX 8 8 ASP A 149 GLY A 172 1 24 HELIX 9 9 THR A 194 GLU A 203 1 10 HELIX 10 10 ARG A 207 GLU A 209 5 3 HELIX 11 11 GLU A 216 MET A 222 1 7 HELIX 12 12 ASN A 226 ALA A 237 1 12 HELIX 13 13 ASP A 263 GLY A 278 1 16 HELIX 14 14 ASP A 294 ASP A 322 1 29 HELIX 15 15 ASP A 322 SER A 332 1 11 HELIX 16 16 ARG A 333 ALA A 338 1 6 HELIX 17 17 GLY A 345 ASP A 352 1 8 HELIX 18 18 ARG A 353 PHE A 356 5 4 HELIX 19 19 ASP A 360 ARG A 367 1 8 HELIX 20 20 ALA A 370 LEU A 383 1 14 SHEET 1 A 8 TYR A 211 VAL A 213 0 SHEET 2 A 8 ARG A 176 ILE A 179 1 N ILE A 179 O GLY A 212 SHEET 3 A 8 THR A 132 ALA A 135 1 N TYR A 133 O ARG A 176 SHEET 4 A 8 MET A 87 THR A 89 1 N ALA A 88 O VAL A 134 SHEET 5 A 8 GLY A 49 HIS A 53 1 N PHE A 52 O THR A 89 SHEET 6 A 8 PHE A 10 GLY A 13 1 N PHE A 12 O THR A 51 SHEET 7 A 8 ARG A 283 PHE A 285 1 O PHE A 285 N THR A 11 SHEET 8 A 8 ASP A 244 LEU A 245 1 N LEU A 245 O HIS A 284 SHEET 1 B 2 GLY A 141 ALA A 142 0 SHEET 2 B 2 ASP A 189 ILE A 190 -1 O ASP A 189 N ALA A 142 LINK O LEU A 57 MG MG A 454 1555 1555 2.70 LINK ND1 HIS A 70 MG MG A 454 1555 1555 2.89 LINK OD1 ASP A 162 MG MG A 453 1555 1555 2.69 LINK OE2BGLU A 180 MN MN A 452 1555 1555 2.25 LINK OE2AGLU A 180 MN MN A 452 1555 1555 1.92 LINK N BARG A 207 MG MG A 453 1555 1555 2.99 LINK N AARG A 207 MG MG A 453 1555 1555 2.91 LINK OH TYR A 211 MG MG A 453 1555 1555 2.79 LINK OE2 GLU A 216 MN A MN A 451 1555 1555 1.94 LINK OE1 GLU A 216 MN B MN A 451 1555 1555 3.11 LINK OE2 GLU A 216 MN B MN A 451 1555 1555 2.10 LINK OE1 GLU A 216 MN C MN A 451 1555 1555 2.97 LINK OE2 GLU A 216 MN C MN A 451 1555 1555 2.47 LINK OE1 GLU A 216 MN MN A 452 1555 1555 2.04 LINK NE2 HIS A 219 MN C MN A 451 1555 1555 1.76 LINK NE2 HIS A 219 MN A MN A 451 1555 1555 2.34 LINK NE2 HIS A 219 MN B MN A 451 1555 1555 3.06 LINK OD2 ASP A 244 MN MN A 452 1555 1555 2.05 LINK OD2AASP A 254 MN A MN A 451 1555 1555 1.97 LINK OD1AASP A 254 MN A MN A 451 1555 1555 2.32 LINK OD2BASP A 254 MN B MN A 451 1555 1555 2.09 LINK OD1BASP A 254 MN B MN A 451 1555 1555 2.85 LINK OD1BASP A 256 MN B MN A 451 1555 1555 1.68 LINK OD1AASP A 256 MN A MN A 451 1555 1555 2.30 LINK OD2BASP A 256 MN B MN A 451 1555 1555 2.95 LINK OD2 ASP A 286 MN MN A 452 1555 1555 2.15 LINK MN B MN A 451 O OH A 455 1555 1555 1.74 LINK MN C MN A 451 O OH A 455 1555 1555 1.79 LINK MN A MN A 451 O OH A 455 1555 1555 2.20 LINK MN C MN A 451 O HOH A 589 1555 1555 2.65 LINK MG MG A 453 O HOH A 829 1555 1555 2.79 LINK MG MG A 454 O HOH A 539 1555 1555 2.75 CISPEP 1 GLU A 185 PRO A 186 0 21.02 SITE 1 AC1 8 GLU A 216 HIS A 219 ASN A 246 ASP A 254 SITE 2 AC1 8 ASP A 256 OH A 455 HOH A 589 HOH A 788 SITE 1 AC2 5 GLU A 180 GLU A 216 ASP A 244 ASP A 286 SITE 2 AC2 5 HOH A 788 SITE 1 AC3 5 ASP A 162 GLU A 206 ARG A 207 TYR A 211 SITE 2 AC3 5 HOH A 829 SITE 1 AC4 4 PRO A 35 LEU A 57 HIS A 70 HOH A 539 SITE 1 AC5 7 GLU A 216 HIS A 219 ASP A 254 ASP A 256 SITE 2 AC5 7 ASP A 286 MN A 451 HOH A 788 CRYST1 85.906 92.883 98.321 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011641 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010766 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010171 0.00000