PDB Short entry for 1XYM HEADER ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE)07-DEC-93 1XYM TITLE THE ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING OPENING, AND TITLE 2 ISOMERIZATION BY D-XYLOSE ISOMERASE: REPLACEMENT OF A CATALYTIC METAL TITLE 3 BY AN AMINO-ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A, B; 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 KEYWDS ISOMERASE(INTRAMOLECULAR OXIDOREDUCTASE) EXPDTA X-RAY DIFFRACTION AUTHOR K.N.ALLEN,A.LAVIE,G.A.PETSKO,D.RINGE REVDAT 7 29-JUL-20 1XYM 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 SITE REVDAT 6 08-JUL-20 1XYM 1 SEQADV REVDAT 5 29-NOV-17 1XYM 1 HELIX REVDAT 4 13-JUL-11 1XYM 1 VERSN REVDAT 3 24-FEB-09 1XYM 1 VERSN REVDAT 2 01-APR-03 1XYM 1 JRNL REVDAT 1 31-MAY-94 1XYM 0 JRNL AUTH K.N.ALLEN,A.LAVIE,A.GLASFELD,T.N.TANADA,D.P.GERRITY, JRNL AUTH 2 S.C.CARLSON,G.K.FARBER,G.A.PETSKO,D.RINGE JRNL TITL ROLE OF THE DIVALENT METAL ION IN SUGAR BINDING, RING JRNL TITL 2 OPENING, AND ISOMERIZATION BY D-XYLOSE ISOMERASE: JRNL TITL 3 REPLACEMENT OF A CATALYTIC METAL BY AN AMINO ACID. JRNL REF BIOCHEMISTRY V. 33 1488 1994 JRNL REFN ISSN 0006-2960 JRNL PMID 7906142 JRNL DOI 10.1021/BI00172A027 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.N.ALLEN,A.LAVIE,G.K.FARBER,A.GLASFELD,G.A.PETSKO,D.RINGE REMARK 1 TITL ISOTOPIC EXCHANGE PLUS SUBSTRATE AND INHIBITION KINETICS OF REMARK 1 TITL 2 D-XYLOSE ISOMERASE DO NOT SUPPORT A PROTON-TRANSFER REMARK 1 TITL 3 MECHANISM REMARK 1 REF BIOCHEMISTRY V. 33 1481 1994 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.LAVIE,K.N.ALLEN,G.A.PETSKO,D.RINGE REMARK 1 TITL X-RAY CRYSTALLOGRAPHIC STRUCTURES OF D-XYLOSE REMARK 1 TITL 2 ISOMERASE-SUBSTRATE COMPLEXES POSITION THE SUBSTRATE AND REMARK 1 TITL 3 PROVIDE EVIDENCE FOR METAL MOVEMENT DURING CATALYSIS REMARK 1 REF TO BE PUBLISHED REMARK 1 REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.197 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6048 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 472 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 2.686 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.77 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.163 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XYM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000177331. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 44.06000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.76500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 44.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.76500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 33060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46350 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -170.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 HZ2 LYS B 599 H2 HOH B 1381 1.20 REMARK 500 HZ2 LYS B 680 HO4 GLO B 960 1.25 REMARK 500 HH11 ARG B 620 H2 HOH B 1174 1.27 REMARK 500 HZ3 LYS A 180 HO4 GLO A 950 1.31 REMARK 500 HH12 ARG A 291 H2 HOH A 1200 1.31 REMARK 500 HH12 ARG B 791 H1 HOH A 1055 1.34 REMARK 500 H ARG B 873 H2 HOH B 1218 1.35 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 HIS A 48 NE2 HIS A 48 CD2 -0.073 REMARK 500 HIS A 53 NE2 HIS A 53 CD2 -0.070 REMARK 500 HIS A 95 NE2 HIS A 95 CD2 -0.070 REMARK 500 HIS A 284 NE2 HIS A 284 CD2 -0.068 REMARK 500 HIS A 381 NE2 HIS A 381 CD2 -0.071 REMARK 500 HIS B 548 NE2 HIS B 548 CD2 -0.070 REMARK 500 HIS B 570 NE2 HIS B 570 CD2 -0.072 REMARK 500 HIS B 595 NE2 HIS B 595 CD2 -0.067 REMARK 500 HIS B 729 NE2 HIS B 729 CD2 -0.068 REMARK 500 HIS B 881 NE2 HIS B 881 CD2 -0.070 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 TRP A 15 CD1 - CG - CD2 ANGL. DEV. = 7.1 DEGREES REMARK 500 TRP A 15 CE2 - CD2 - CG ANGL. DEV. = -6.0 DEGREES REMARK 500 TRP A 19 CD1 - CG - CD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 TRP A 19 CE2 - CD2 - CG ANGL. DEV. = -5.2 DEGREES REMARK 500 ARG A 22 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 30 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TRP A 136 CD1 - CG - CD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 TRP A 136 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 176 CG - CD - NE ANGL. DEV. = 12.7 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 TRP A 236 CD1 - CG - CD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 TRP A 236 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 258 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -4.9 DEGREES REMARK 500 TRP A 269 CD1 - CG - CD2 ANGL. DEV. = 5.1 DEGREES REMARK 500 TRP A 269 CE2 - CD2 - CG ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 283 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 TRP A 299 CD1 - CG - CD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 TRP A 299 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 ARG A 307 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 307 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 367 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 367 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 386 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR B 502 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 TRP B 515 CD1 - CG - CD2 ANGL. DEV. = 6.7 DEGREES REMARK 500 TRP B 515 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP B 519 CD1 - CG - CD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 TRP B 519 CE2 - CD2 - CG ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG B 530 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG B 573 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 575 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG B 616 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 616 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B 620 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 TRP B 636 CD1 - CG - CD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 TRP B 636 CE2 - CD2 - CG ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG B 651 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 TYR B 673 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR B 711 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 TRP B 736 CD1 - CG - CD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 TRP B 736 CE2 - CD2 - CG ANGL. DEV. = -5.7 DEGREES REMARK 500 TRP B 736 CG - CD2 - CE3 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG B 758 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG B 758 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG B 765 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 62 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 TYR A 2 75.80 40.32 REMARK 500 PRO A 6 -55.96 -8.41 REMARK 500 ARG A 9 50.80 35.05 REMARK 500 PHE A 93 -28.98 -140.99 REMARK 500 GLU A 185 110.26 74.58 REMARK 500 ASN A 246 -160.66 -171.55 REMARK 500 SER A 249 50.63 -100.64 REMARK 500 LYS A 252 -170.95 -176.61 REMARK 500 ALA A 342 70.49 -156.07 REMARK 500 PHE A 356 -71.42 -153.26 REMARK 500 THR B 516 -74.33 -79.37 REMARK 500 PHE B 593 -22.34 -140.32 REMARK 500 GLU B 685 119.79 73.75 REMARK 500 ASN B 746 -163.08 -168.30 REMARK 500 SER B 749 54.99 -105.06 REMARK 500 LYS B 752 -172.20 -171.14 REMARK 500 ALA B 842 70.62 -151.49 REMARK 500 PHE B 856 -67.60 -145.06 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 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 216 OE2 REMARK 620 2 HIS A 219 NE2 80.8 REMARK 620 3 ASP A 254 OD1 101.5 81.7 REMARK 620 4 ASP A 254 OD2 152.2 92.3 50.6 REMARK 620 5 ASP A 256 OD1 82.1 161.1 94.0 99.2 REMARK 620 6 OH A1700 O 103.0 105.2 155.2 104.8 86.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 901 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 716 OE2 REMARK 620 2 HIS B 719 NE2 78.0 REMARK 620 3 ASP B 754 OD1 97.1 79.2 REMARK 620 4 ASP B 754 OD2 147.3 88.9 50.7 REMARK 620 5 ASP B 756 OD1 86.2 161.7 93.9 99.9 REMARK 620 6 OH B1800 O 103.0 111.6 158.7 109.6 80.7 REMARK 620 N 1 2 3 4 5 REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEETS PRESENTED AS *SA1*, *SA2*, *SB1*, AND *SB2* ON REMARK 700 SHEET RECORDS BELOW ARE ACTUALLY EIGHT-STRANDED REMARK 700 BETA-BARRELS. THESE ARE REPRESENTED AS NINE-STRANDED REMARK 700 SHEETS IN WHICH THE FIRST AND LAST STRANDS OF EACH SHEET REMARK 700 ARE IDENTICAL. REMARK 700 THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. REMARK 700 THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE REMARK 700 IDENTICAL STRANDS. SHEETS *SA1* AND *SB1* REPRESENT ONE REMARK 700 BIFURCATED SHEET. SHEETS *SA2* AND *SB2* REPRESENT REMARK 700 ANOTHER BIFURCATED SHEET. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: M1A REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: WHILE THE ACTIVE SITE IN THE WILD TYPE ENZYME REMARK 800 CONTAINS THE METAL BINDING SITE, IN THIS MUTANT THE METAL IONS REMARK 800 IN THESE SITES ARE REPLACED BY THE N-EPSILON AMINO GROUPS OF LYS REMARK 800 REMARK 800 SITE_IDENTIFIER: M2A REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: M1B REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: WHILE THE ACTIVE SITE IN THE WILD TYPE ENZYME REMARK 800 CONTAINS THE METAL BINDING SITE, IN THIS MUTANT THE METAL IONS REMARK 800 IN THESE SITES ARE REPLACED BY THE N-EPSILON AMINO GROUPS OF LYS REMARK 800 REMARK 800 SITE_IDENTIFIER: M2B REMARK 800 EVIDENCE_CODE: AUTHOR REMARK 800 SITE_DESCRIPTION: METAL BINDING SITE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE REPORTED HERE DISAGREES WITH THAT ORIGINALLY REMARK 999 REPORTED (FARBER ET AL., BIOCHEMISTRY V. 28, P. 7289, REMARK 999 1989) AND FOUND AS SWISS-PROT: XYLA_STROL AND PIR: S28986. REMARK 999 A TOTAL OF 13 AMINO ACIDS WERE CHANGED, OF WHICH 5 WERE IN REMARK 999 THE C-TERMINAL DOMAIN. THE AUTHORS STATE THAT THIS REMARK 999 CORRECTED SEQUENCE WILL BE INCLUDED IN THE SPRING 1994 REMARK 999 RELEASES OF THE SEQUENCE DATA BASES. SEE REFERENCE 2 REMARK 999 ABOVE FOR MORE INFORMATION. DBREF 1XYM A 1 386 UNP P15587 XYLA_STROL 1 386 DBREF 1XYM B 501 886 UNP P15587 XYLA_STROL 1 386 SEQADV 1XYM LYS A 180 UNP P15587 GLU 180 CONFLICT SEQADV 1XYM LYS B 680 UNP P15587 GLU 180 CONFLICT 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 THR ARG PHE ALA ILE LYS 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 SEQRES 1 B 386 SER TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY SEQRES 2 B 386 LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY SEQRES 3 B 386 ASP ALA THR ARG PRO ALA LEU ASP PRO VAL GLU THR VAL SEQRES 4 B 386 GLN ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE SEQRES 5 B 386 HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP THR SEQRES 6 B 386 GLU ARG GLU SER HIS ILE LYS ARG PHE ARG GLN ALA LEU SEQRES 7 B 386 ASP ALA THR GLY MET THR VAL PRO MET ALA THR THR ASN SEQRES 8 B 386 LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR SEQRES 9 B 386 ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS SEQRES 10 B 386 THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA SEQRES 11 B 386 LYS THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SEQRES 12 B 386 SER GLY ALA ALA LYS ASP VAL ARG VAL ALA LEU ASP ARG SEQRES 13 B 386 MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SEQRES 14 B 386 SER GLN GLY TYR ASP THR ARG PHE ALA ILE LYS PRO LYS SEQRES 15 B 386 PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL SEQRES 16 B 386 GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO SEQRES 17 B 386 GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN SEQRES 18 B 386 MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA SEQRES 19 B 386 LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY SEQRES 20 B 386 GLN SER GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY SEQRES 21 B 386 ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU SEQRES 22 B 386 LEU GLU SER ALA GLY TYR GLU GLY PRO ARG HIS PHE ASP SEQRES 23 B 386 PHE LYS PRO PRO ARG THR GLU ASP ILE ASP GLY VAL TRP SEQRES 24 B 386 ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU SEQRES 25 B 386 LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL SEQRES 26 B 386 GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA SEQRES 27 B 386 GLN PRO THR ALA ALA ASP GLY VAL GLN GLU LEU LEU ALA SEQRES 28 B 386 ASP ARG THR ALA PHE GLU ASP PHE ASP VAL ASP ALA ALA SEQRES 29 B 386 ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU SEQRES 30 B 386 ALA MET ASP HIS LEU LEU GLY ALA ARG HET GLO A 950 24 HET MG A 401 1 HET OH A1700 2 HET GLO B 960 24 HET MG B 901 1 HET OH B1800 2 HETNAM GLO D-GLUCOSE HETNAM MG MAGNESIUM ION HETNAM OH HYDROXIDE ION FORMUL 3 GLO 2(C6 H12 O6) FORMUL 4 MG 2(MG 2+) FORMUL 5 OH 2(H O 1-) FORMUL 9 HOH *472(H2 O) HELIX 1 H1 LEU A 14 TRP A 19 1IN ALPHA/BETA BARREL 6 HELIX 2 H2 PRO A 35 LEU A 45 1IN ALPHA/BETA BARREL 11 HELIX 3 H3 ASP A 64 THR A 81 1IN ALPHA/BETA BARREL 18 HELIX 4 H4 ARG A 108 LEU A 128 1IN ALPHA/BETA BARREL 21 HELIX 5 H5 VAL A 150 GLN A 171 1IN ALPHA/BETA BARREL 22 HELIX 6 H6 VAL A 195 ARG A 204 1IN ALPHA/BETA BARREL 10 HELIX 7 H7 VAL A 217 ALA A 223 1IN ALPHA/BETA BARREL 7 HELIX 8 H8 PHE A 227 ALA A 237 1IN ALPHA/BETA BARREL 11 HELIX 9 H9 ARG A 265 SER A 276 1IN ALPHA/BETA BARREL 12 HELIX 10 H10 ILE A 295 ALA A 321 1IN ALPHA/BETA BARREL 27 HELIX 11 H11 GLU A 324 ALA A 331 1IN ALPHA/BETA BARREL 8 HELIX 12 H12 LEU A 334 ALA A 338 1IN ALPHA/BETA BARREL 5 HELIX 13 H13 VAL A 346 ASP A 352 1IN ALPHA/BETA BARREL 7 HELIX 14 H14 VAL A 361 ALA A 366 1IN ALPHA/BETA BARREL 6 HELIX 15 H15 PHE A 371 LEU A 382 1IN ALPHA/BETA BARREL 12 HELIX 16 H16 LEU B 514 TRP B 519 1IN ALPHA/BETA BARREL 6 HELIX 17 H17 PRO B 535 LEU B 545 1IN ALPHA/BETA BARREL 11 HELIX 18 H18 ASP B 564 THR B 581 1IN ALPHA/BETA BARREL 18 HELIX 19 H19 ARG B 608 LEU B 628 1IN ALPHA/BETA BARREL 21 HELIX 20 H20 VAL B 650 GLN B 671 1IN ALPHA/BETA BARREL 22 HELIX 21 H21 VAL B 695 ARG B 704 1IN ALPHA/BETA BARREL 10 HELIX 22 H22 VAL B 717 ALA B 723 1IN ALPHA/BETA BARREL 7 HELIX 23 H23 PHE B 727 ALA B 737 1IN ALPHA/BETA BARREL 11 HELIX 24 H24 ARG B 765 SER B 776 1IN ALPHA/BETA BARREL 12 HELIX 25 H25 ILE B 795 ALA B 821 1IN ALPHA/BETA BARREL 27 HELIX 26 H26 GLU B 824 ALA B 831 1IN C-TERMINAL DOMAIN 8 HELIX 27 H27 LEU B 834 ALA B 838 1IN C-TERMINAL DOMAIN 5 HELIX 28 H28 VAL B 846 ASP B 852 1IN C-TERMINAL DOMAIN 7 HELIX 29 H29 VAL B 861 ALA B 866 1IN C-TERMINAL DOMAIN 6 HELIX 30 H30 PHE B 871 LEU B 882 1IN C-TERMINAL DOMAIN 12 SHEET 1 SA1 9 PHE A 10 GLY A 13 0 SHEET 2 SA1 9 GLY A 49 HIS A 53 1 SHEET 3 SA1 9 THR A 84 THR A 90 1 SHEET 4 SA1 9 THR A 132 GLY A 138 1 SHEET 5 SA1 9 ARG A 176 PRO A 183 1 SHEET 6 SA1 9 TYR A 211 GLU A 216 1 SHEET 7 SA1 9 PHE A 241 ASN A 246 1 SHEET 8 SA1 9 ARG A 283 ASP A 286 1 SHEET 9 SA1 9 PHE A 10 GLY A 13 1 SHEET 1 SA2 9 PHE A 10 GLY A 13 0 SHEET 2 SA2 9 GLY A 49 HIS A 53 1 SHEET 3 SA2 9 THR A 84 THR A 90 1 SHEET 4 SA2 9 GLU A 140 GLU A 143 1 SHEET 5 SA2 9 ARG A 176 PRO A 183 1 SHEET 6 SA2 9 TYR A 211 GLU A 216 1 SHEET 7 SA2 9 PHE A 241 ASN A 246 1 SHEET 8 SA2 9 GLY A 278 GLY A 281 1 SHEET 9 SA2 9 PHE A 10 GLY A 13 1 SHEET 1 SB1 9 PHE B 510 GLY B 513 0 SHEET 2 SB1 9 GLY B 549 HIS B 553 1 SHEET 3 SB1 9 THR B 584 THR B 590 1 SHEET 4 SB1 9 THR B 632 GLY B 638 1 SHEET 5 SB1 9 ARG B 676 PRO B 683 1 SHEET 6 SB1 9 TYR B 711 GLU B 716 1 SHEET 7 SB1 9 PHE B 741 ASN B 746 1 SHEET 8 SB1 9 ARG B 783 ASP B 786 1 SHEET 9 SB1 9 PHE B 510 GLY B 513 1 SHEET 1 SB2 9 PHE B 510 GLY B 513 0 SHEET 2 SB2 9 GLY B 549 HIS B 553 1 SHEET 3 SB2 9 THR B 584 THR B 590 1 SHEET 4 SB2 9 GLU B 640 GLU B 643 1 SHEET 5 SB2 9 ARG B 676 PRO B 683 1 SHEET 6 SB2 9 TYR B 711 GLU B 716 1 SHEET 7 SB2 9 PHE B 741 ASN B 746 1 SHEET 8 SB2 9 GLY B 778 GLY B 781 1 SHEET 9 SB2 9 PHE B 510 GLY B 513 1 LINK OE2 GLU A 216 MG MG A 401 1555 1555 2.42 LINK NE2 HIS A 219 MG MG A 401 1555 1555 2.66 LINK OD1 ASP A 254 MG MG A 401 1555 1555 2.69 LINK OD2 ASP A 254 MG MG A 401 1555 1555 2.39 LINK OD1 ASP A 256 MG MG A 401 1555 1555 2.44 LINK MG MG A 401 O OH A1700 1555 1555 1.94 LINK OE2 GLU B 716 MG MG B 901 1555 1555 2.44 LINK NE2 HIS B 719 MG MG B 901 1555 1555 2.80 LINK OD1 ASP B 754 MG MG B 901 1555 1555 2.73 LINK OD2 ASP B 754 MG MG B 901 1555 1555 2.34 LINK OD1 ASP B 756 MG MG B 901 1555 1555 2.41 LINK MG MG B 901 O OH B1800 1555 1555 1.93 CISPEP 1 GLU A 185 PRO A 186 0 14.42 CISPEP 2 GLU B 685 PRO B 686 0 5.24 SITE 1 M1A 5 LYS A 180 ASP A 244 ASP A 286 GLU A 216 SITE 2 M1A 5 GLO A 950 SITE 1 M2A 6 MG A 401 GLU A 216 HIS A 219 ASP A 254 SITE 2 M2A 6 ASP A 256 OH A1700 SITE 1 M1B 5 LYS B 680 ASP B 744 ASP B 786 GLU B 716 SITE 2 M1B 5 GLO B 960 SITE 1 M2B 6 MG B 901 GLU B 716 HIS B 719 ASP B 754 SITE 2 M2B 6 ASP B 756 OH B1800 CRYST1 88.120 99.530 94.790 90.00 90.00 90.00 P 21 21 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 0.011348 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010047 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010550 0.00000 MTRIX1 1 0.999270 0.038290 -0.000450 -0.02028 1 MTRIX2 1 0.038290 -0.999270 0.001000 0.02478 1 MTRIX3 1 -0.000410 -0.001020 -1.000000 -47.31872 1