PDB Short entry for 4A8L HEADER ISOMERASE 21-NOV-11 4A8L TITLE PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE CRYSTALS TITLE 2 GROWN DURING THE PCDF-PROTEIN MISSION COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-XYLOSE KETOL ISOMERASE; COMPND 5 EC: 5.3.1.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929 KEYWDS ISOMERASE, MICROGRAVITY EXPDTA X-RAY DIFFRACTION AUTHOR K.DECANNIERE,L.-D.PATINO-LOPEZ,M.SLEUTEL,C.EVRARD,C.VAN DE WEERDT, AUTHOR 2 E.HAUMONT,J.A.GAVIRA,F.OTALORA,D.MAES REVDAT 1 30-NOV-11 4A8L 0 JRNL AUTH K.DECANNIERE,L.-D.PATINO-LOPEZ,M.SLEUTEL,C.EVRARD, JRNL AUTH 2 C.VAN DE WEERDT,E.HAUMONT,J.A.GAVIRA,F.OTALORA,D.MAES JRNL TITL PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE JRNL TITL 2 CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 70.87 REMARK 3 DATA CUTOFF (SIGMA(F)) : NONE REMARK 3 COMPLETENESS FOR RANGE (%) : 99.84 REMARK 3 NUMBER OF REFLECTIONS : 96519 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.11142 REMARK 3 R VALUE (WORKING SET) : 0.11007 REMARK 3 FREE R VALUE : 0.13676 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.0 REMARK 3 FREE R VALUE TEST SET COUNT : 5124 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.351 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.386 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6951 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.49 REMARK 3 BIN R VALUE (WORKING SET) : 0.076 REMARK 3 BIN FREE R VALUE SET COUNT : 412 REMARK 3 BIN FREE R VALUE : 0.128 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3218 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 489 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.910 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02 REMARK 3 B22 (A**2) : 0.25 REMARK 3 B33 (A**2) : -0.23 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.037 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.037 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.017 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.882 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.976 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3295 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4507 ; 2.194 ; 1.957 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 439 ; 5.704 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;33.409 ;23.086 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 524 ;11.094 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.007 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 467 ; 0.127 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2677 ; 0.016 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2027 ; 2.422 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3257 ; 3.239 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1268 ; 4.345 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1231 ; 5.627 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 3295 ; 2.694 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 493 ;13.568 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 3191 ; 6.561 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE REMARK 3 RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. REMARK 4 REMARK 4 4A8L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-NOV-11. REMARK 100 THE PDBE ID CODE IS EBI-50390. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 13 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM16 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.977 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 197146 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.35 REMARK 200 RESOLUTION RANGE LOW (A) : 24.60 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 46 REMARK 200 R MERGE (I) : 0.05 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 69.00 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 23 REMARK 200 R MERGE FOR SHELL (I) : 0.13 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 31.00 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2GLK REMARK 200 REMARK 200 REMARK: STRUCTURE FACTOR FILE HAS DATA TILL 0.977 ANGSTROM. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.7 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32.7 MG/ML PROTEIN, 0.6 M REMARK 280 AMMONIUM SULPHATE, 100 MM HEPES PH 7.0 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 46.28000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.21000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.06500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.28000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.21000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.06500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.28000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.21000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.06500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.28000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.21000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.06500 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 REMARK 350 TOTAL BURIED SURFACE AREA: 32210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 46250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -220.5 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 0.00000 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 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 GLY A 388 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASN A 2 CG OD1 ND2 REMARK 470 GLU A 8 CG CD OE1 OE2 REMARK 470 ARG A 10 CD NE CZ NH1 NH2 REMARK 470 ARG A 32 NE CZ NH1 NH2 REMARK 470 ARG A 41 NE CZ NH1 NH2 REMARK 470 GLU A 132 CG CD OE1 OE2 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 O HOH A 2210 O HOH A 2211 1.93 REMARK 500 OE2 GLU A 328 O HOH A 2409 1.94 REMARK 500 O HOH A 2009 O HOH A 2011 2.17 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 ASP A 24 C PRO A 25 N 0.194 REMARK 500 ARG A 76 CZ ARG A 76 NH2 -0.086 REMARK 500 LYS A 85 CE LYS A 85 NZ 0.206 REMARK 500 GLU A 128 CG GLU A 128 CD 0.120 REMARK 500 GLU A 181 CD GLU A 181 OE2 0.079 REMARK 500 GLU A 204 CD GLU A 204 OE2 0.079 REMARK 500 ASP A 255 CB ASP A 255 CG -0.175 REMARK 500 ARG A 266 NE ARG A 266 CZ 0.086 REMARK 500 ARG A 266 CZ ARG A 266 NH2 -0.105 REMARK 500 PHE A 296 CD1 PHE A 296 CE1 0.130 REMARK 500 ARG A 340 CG ARG A 340 CD 0.177 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 ASP A 81 CB - CG - OD1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 177 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 GLU A 217 OE1 - CD - OE2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP A 255 OD1 - CG - OD2 ANGL. DEV. = -15.1 DEGREES REMARK 500 ASP A 255 CB - CG - OD1 ANGL. DEV. = 12.8 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 PHE A 296 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 GLU A 337 CG - CD - OE1 ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 374 NE - CZ - NH1 ANGL. DEV. = -8.9 DEGREES REMARK 500 ARG A 374 NE - CZ - NH2 ANGL. DEV. = 7.5 DEGREES 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 17 -75.29 -84.71 REMARK 500 PHE A 94 -25.48 -140.73 REMARK 500 ASP A 175 76.30 -108.11 REMARK 500 GLU A 186 100.75 83.67 REMARK 500 ASN A 247 -169.14 -167.83 REMARK 500 ALA A 343 61.74 -151.75 REMARK 500 PHE A 357 -75.12 -154.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 24 15.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 1,2-ETHANEDIOL (EDO): TENTATIVE REMARK 600 COBALT (II) ION (CO): COBALT MOST LIKELY GIVEN ANOMALOUS REMARK 600 EFFECT AT DIFFERENT WAVELENGTHS 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 CO A1389 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 97.3 REMARK 620 3 ASP A 245 OD2 91.9 104.8 REMARK 620 4 ASP A 287 OD2 161.0 87.1 104.9 REMARK 620 5 EDO A1388 O2 85.9 167.7 86.9 86.3 REMARK 620 6 HOH A2277 O 83.8 96.9 158.3 77.3 71.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CO A1390 CO REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 255 OD2 REMARK 620 2 ASP A 257 OD1 98.5 REMARK 620 3 HOH A2301 O 99.1 75.2 REMARK 620 4 GLU A 217 OE2 161.0 90.7 99.4 REMARK 620 5 ASP A 255 OD1 55.4 86.9 146.6 108.9 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 EDO A1388 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A1389 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO A1390 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1GW9 RELATED DB: PDB REMARK 900 TRI-IODIDE DERIVATIVE OF XYLOSE ISOMERASE FROM REMARK 900 STREPTOMYCES RUBIGINOSUS REMARK 900 RELATED ID: 1OAD RELATED DB: PDB REMARK 900 GLUCOSE ISOMERASE FROM STREPTOMYCES RUBIGINOSUS IN P21212 REMARK 900 CRYSTAL FORM REMARK 900 RELATED ID: 1XIB RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE (PH 7.4) REMARK 900 RELATED ID: 1XIJ RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH THREONATE AND MN (PH REMARK 900 9.0) REMARK 900 RELATED ID: 1XIE RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH 1,5-DIANHYDROSORBITOL REMARK 900 (PH 7.4) REMARK 900 RELATED ID: 4A8I RELATED DB: PDB REMARK 900 PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE REMARK 900 CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION REMARK 900 RELATED ID: 1XIC RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH D-XYLOSE (PH 9.0) REMARK 900 RELATED ID: 3XIS RELATED DB: PDB REMARK 900 XYLOSE ISOMERASE COMPLEX WITH XYLOSE REMARK 900 RELATED ID: 2GLK RELATED DB: PDB REMARK 900 HIGH-RESOLUTION STUDY OF D-XYLOSE ISOMERASE, 0. REMARK 900 94ARESOLUTION. REMARK 900 RELATED ID: 1MNZ RELATED DB: PDB REMARK 900 ATOMIC STRUCTURE OF GLUCOSE ISOMERASE REMARK 900 RELATED ID: 1XII RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH 300MM D-XYLULOSE AND REMARK 900 MN (PH 8.0) REMARK 900 RELATED ID: 1XIF RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH GLUCOSE, MN, AND MG REMARK 900 (PH 8.0) REMARK 900 RELATED ID: 2XIS RELATED DB: PDB REMARK 900 XYLOSE ISOMERASE COMPLEX WITH XYLITOL REMARK 900 RELATED ID: 1XIS RELATED DB: PDB REMARK 900 XYLOSE ISOMERASE COMPLEX WITH MNCL2 REMARK 900 RELATED ID: 9XIA RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEX WITH INACTIVATOR REMARK 900 RELATED ID: 1XID RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH L-ASCORBIC ACID, MN REMARK 900 , AND MG (PH 7.4) REMARK 900 RELATED ID: 1O1H RELATED DB: PDB REMARK 900 STRUCTURE OF GLUCOSE ISOMERASE DERIVATIZED WITH KR. REMARK 900 RELATED ID: 1XIG RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH XYLITOL, MG, AND MN REMARK 900 (PH 7.4) REMARK 900 RELATED ID: 2GVE RELATED DB: PDB REMARK 900 TIME-OF-FLIGHT NEUTRON DIFFRACTION STRUCTURE OF D- REMARK 900 XYLOSEISOMERASE REMARK 900 RELATED ID: 4XIS RELATED DB: PDB REMARK 900 XYLOSE ISOMERASE COMPLEX WITH XYLOSE AND MNCL2 REMARK 900 RELATED ID: 8XIA RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEX WITH D-XYLOSE REMARK 900 RELATED ID: 2GUB RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF METAL FREE D-XYLOSE ISOMERASE. REMARK 900 RELATED ID: 1XIH RELATED DB: PDB REMARK 900 D-XYLOSE ISOMERASE COMPLEXED WITH D-SORBITOL AND NO REMARK 900 ADDED MN (PH 9.0) REMARK 900 RELATED ID: 4A8R RELATED DB: PDB REMARK 900 PROTEIN CRYSTALLIZATION AND MICROGRAVITY: GLUCOSE ISOMERASE REMARK 900 CRYSTALS GROWN DURING THE PCDF-PROTEIN MISSION DBREF 4A8L A 1 388 UNP P24300 XYLA_STRRU 1 388 SEQRES 1 A 388 MET ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE SEQRES 2 A 388 GLY LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE SEQRES 3 A 388 GLY ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER SEQRES 4 A 388 VAL ARG ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR SEQRES 5 A 388 PHE HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SEQRES 6 A 388 SER GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA SEQRES 7 A 388 LEU ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR SEQRES 8 A 388 ASN LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE SEQRES 9 A 388 THR ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG SEQRES 10 A 388 LYS THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY SEQRES 11 A 388 ALA GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA SEQRES 12 A 388 GLU SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP SEQRES 13 A 388 ARG MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL SEQRES 14 A 388 THR SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO SEQRES 15 A 388 LYS PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR SEQRES 16 A 388 VAL GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG SEQRES 17 A 388 PRO GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU SEQRES 18 A 388 GLN MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN SEQRES 19 A 388 ALA LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN SEQRES 20 A 388 GLY GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE SEQRES 21 A 388 GLY ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP SEQRES 22 A 388 LEU LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE SEQRES 23 A 388 ASP PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL SEQRES 24 A 388 TRP ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE SEQRES 25 A 388 LEU LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU SEQRES 26 A 388 VAL GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU SEQRES 27 A 388 ALA ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU SEQRES 28 A 388 ASP ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA SEQRES 29 A 388 ALA ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN SEQRES 30 A 388 LEU ALA MET ASP HIS LEU LEU GLY ALA ARG GLY HET EDO A1388 4 HET CO A1389 1 HET CO A1390 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM CO COBALT (II) ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 CO 2(CO 2+) FORMUL 4 HOH *489(H2 O) HELIX 1 1 THR A 6 ASP A 9 5 4 HELIX 2 2 LEU A 15 GLY A 19 1 5 HELIX 3 3 ASP A 35 GLY A 47 1 13 HELIX 4 4 ASP A 55 ILE A 59 1 5 HELIX 5 5 SER A 64 GLY A 83 1 20 HELIX 6 6 HIS A 96 LYS A 100 5 5 HELIX 7 7 ASP A 108 LEU A 129 1 22 HELIX 8 8 ASP A 150 GLY A 173 1 24 HELIX 9 9 THR A 195 GLU A 204 1 10 HELIX 10 10 ARG A 208 GLU A 210 5 3 HELIX 11 11 GLU A 217 MET A 223 1 7 HELIX 12 12 ASN A 227 ALA A 238 1 12 HELIX 13 13 ASP A 264 GLY A 279 1 16 HELIX 14 14 ASP A 295 ASP A 323 1 29 HELIX 15 15 ASP A 323 SER A 333 1 11 HELIX 16 16 ARG A 334 ALA A 339 1 6 HELIX 17 17 GLY A 346 ASP A 352 1 7 HELIX 18 18 ASP A 353 PHE A 357 5 5 HELIX 19 19 ASP A 361 ARG A 368 1 8 HELIX 20 20 ALA A 371 GLY A 385 1 15 SHEET 1 AA 8 TYR A 212 VAL A 214 0 SHEET 2 AA 8 ARG A 177 ILE A 180 1 O PHE A 178 N GLY A 213 SHEET 3 AA 8 THR A 133 ALA A 136 1 O TYR A 134 N ALA A 179 SHEET 4 AA 8 MET A 88 THR A 90 1 O ALA A 89 N VAL A 135 SHEET 5 AA 8 GLY A 50 HIS A 54 1 O PHE A 53 N THR A 90 SHEET 6 AA 8 PHE A 11 GLY A 14 1 O PHE A 13 N THR A 52 SHEET 7 AA 8 ARG A 284 PHE A 286 1 O ARG A 284 N THR A 12 SHEET 8 AA 8 ASP A 245 LEU A 246 1 N LEU A 246 O HIS A 285 SHEET 1 AB 2 GLY A 142 ALA A 143 0 SHEET 2 AB 2 ASP A 190 ILE A 191 -1 O ASP A 190 N ALA A 143 LINK C2 EDO A1388 CO CO A1389 1555 1555 3.33 LINK O2 EDO A1388 CO CO A1389 1555 1555 2.36 LINK CO CO A1389 OE2 GLU A 181 1555 1555 2.14 LINK CO CO A1389 OE1 GLU A 217 1555 1555 2.10 LINK CO CO A1389 OD2 ASP A 245 1555 1555 2.31 LINK CO CO A1389 OD2 ASP A 287 1555 1555 2.11 LINK CO CO A1389 O HOH A2277 1555 1555 2.40 LINK CO CO A1390 OD1 ASP A 257 1555 1555 2.50 LINK CO CO A1390 O HOH A2301 1555 1555 2.12 LINK CO CO A1390 OE2 GLU A 217 1555 1555 2.04 LINK CO CO A1390 OD1 ASP A 255 1555 1555 2.13 LINK CO CO A1390 OD2 ASP A 255 1555 1555 2.35 CISPEP 1 GLU A 186 PRO A 187 0 20.09 SITE 1 AC1 9 HIS A 54 TRP A 137 GLU A 181 ASP A 245 SITE 2 AC1 9 ASP A 287 CO A1389 HOH A2160 HOH A2277 SITE 3 AC1 9 HOH A2331 SITE 1 AC2 6 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 2 AC2 6 EDO A1388 HOH A2277 SITE 1 AC3 5 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC3 5 HOH A2301 CRYST1 92.560 98.420 102.130 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 0.010804 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010161 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009791 0.00000