HEADER ISOMERASE 21-JAN-04 1S5M TITLE XYLOSE ISOMERASE IN SUBSTRATE AND INHIBITOR MICHAELIS STATES: ATOMIC TITLE 2 RESOLUTION STUDIES OF A METAL-MEDIATED HYDRIDE SHIFT 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 GENE: XYLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HB101; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PX15 KEYWDS XYLOSE ISOMERASE, HYDRIDE SHIFT, ATOMIC RESOLUTION, TIM BARREL, KEYWDS 2 ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR T.D.FENN,D.RINGE,G.A.PETSKO REVDAT 8 23-AUG-23 1S5M 1 HETSYN REVDAT 7 29-JUL-20 1S5M 1 COMPND REMARK HETNAM LINK REVDAT 7 2 1 SITE REVDAT 6 24-JUL-19 1S5M 1 REMARK REVDAT 5 31-JAN-18 1S5M 1 REMARK REVDAT 4 13-JUL-11 1S5M 1 VERSN REVDAT 3 24-FEB-09 1S5M 1 VERSN REVDAT 2 22-JUN-04 1S5M 1 JRNL REVDAT 1 10-FEB-04 1S5M 0 JRNL AUTH T.D.FENN,D.RINGE,G.A.PETSKO JRNL TITL XYLOSE ISOMERASE IN SUBSTRATE AND INHIBITOR MICHAELIS JRNL TITL 2 STATES: ATOMIC RESOLUTION STUDIES OF A METAL-MEDIATED JRNL TITL 3 HYDRIDE SHIFT(,). JRNL REF BIOCHEMISTRY V. 43 6464 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15157080 JRNL DOI 10.1021/BI049812O REMARK 2 REMARK 2 RESOLUTION. 0.98 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) : 0.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 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) : 0.111 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.111 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.129 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 10601 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 212189 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)) : 0.098 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)) : 8706 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 174294 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 : 16 REMARK 3 SOLVENT ATOMS : 411 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3448.3 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2924.7 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 58 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 33226 REMARK 3 NUMBER OF RESTRAINTS : 43898 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.017 REMARK 3 ANGLE DISTANCES (A) : 0.032 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.101 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.101 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.095 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.006 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.048 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.105 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: ANISOTROPIC REFINEMENT REDUCED FREE R REMARK 3 (NO CUTOFF) BY 2.3% REMARK 4 REMARK 4 1S5M COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-04. REMARK 100 THE DEPOSITION ID IS D_1000021396. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI-111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 212189 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.980 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.6 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.47300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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: STREPTOMYCES OLIVOCHROMOGENES XYLOSE ISOMERASE - REMARK 200 PDB ID 1XYA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.1M (NH4)2SO4, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 398K, TEMPERATURE 298.0K 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 42.93250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.48400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.14900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.93250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.48400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.14900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.93250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.48400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.14900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.93250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.48400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.14900 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: 33790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -263.0 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 92.96800 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 92.96800 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 A2142 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2253 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2333 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2368 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 OD2 ASP A 344 OE1 GLU A 348 1.12 REMARK 500 OD2 ASP A 344 CD GLU A 348 1.68 REMARK 500 CG ASP A 344 OE1 GLU A 348 2.08 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 73 CZ ARG A 73 NH1 0.096 REMARK 500 ARG A 73 CZ ARG A 73 NH2 0.099 REMARK 500 HIS A 95 NE2 HIS A 95 CD2 -0.077 REMARK 500 ARG A 315 CZ ARG A 315 NH2 0.081 REMARK 500 GLU A 336 CB GLU A 336 CG -0.172 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 ARG A 9 NE - CZ - NH1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ARG A 9 NE - CZ - NH2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 64 CB - CG - OD1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 73 CD - NE - CZ ANGL. DEV. = 46.8 DEGREES REMARK 500 ARG A 75 CD - NE - CZ ANGL. DEV. = 9.6 DEGREES REMARK 500 ARG A 108 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG A 120 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 120 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 GLU A 127 OE1 - CD - OE2 ANGL. DEV. = 13.6 DEGREES REMARK 500 ASP A 149 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 151 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 TYR A 173 CB - CG - CD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 174 N - CA - CB ANGL. DEV. = -11.1 DEGREES REMARK 500 ASP A 174 CB - CG - OD1 ANGL. DEV. = -6.2 DEGREES REMARK 500 ASP A 174 CB - CG - OD1 ANGL. DEV. = 11.7 DEGREES REMARK 500 ASP A 174 CB - CG - OD2 ANGL. DEV. = -13.5 DEGREES REMARK 500 ASP A 174 O - C - N ANGL. DEV. = -11.1 DEGREES REMARK 500 ARG A 176 NH1 - CZ - NH2 ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 ARG A 176 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 176 NE - CZ - NH2 ANGL. DEV. = -6.1 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 187 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 204 CD - NE - CZ ANGL. DEV. = 25.7 DEGREES REMARK 500 ARG A 204 CD - NE - CZ ANGL. DEV. = 19.7 DEGREES REMARK 500 ARG A 204 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 204 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 207 NE - CZ - NH2 ANGL. DEV. = -4.4 DEGREES REMARK 500 TYR A 211 CB - CG - CD2 ANGL. DEV. = 6.6 DEGREES REMARK 500 TYR A 211 CB - CG - CD1 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 265 CG - CD - NE ANGL. DEV. = 27.3 DEGREES REMARK 500 ARG A 265 CD - NE - CZ ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG A 265 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 265 NE - CZ - NH2 ANGL. DEV. = -7.6 DEGREES REMARK 500 ARG A 283 NE - CZ - NH1 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 315 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG A 315 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 GLU A 324 OE1 - CD - OE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 VAL A 346 CA - CB - CG1 ANGL. DEV. = 10.3 DEGREES REMARK 500 ARG A 353 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 GLU A 357 OE1 - CD - OE2 ANGL. DEV. = -9.1 DEGREES REMARK 500 ARG A 367 NE - CZ - NH2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 373 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 373 NE - CZ - NH2 ANGL. DEV. = 6.6 DEGREES REMARK 500 ARG A 386 NE - CZ - NH1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 386 NE - CZ - NH2 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG A 386 NE - CZ - NH2 ANGL. DEV. = -5.3 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 16 -77.47 -83.01 REMARK 500 PHE A 93 -28.81 -141.45 REMARK 500 GLU A 185 103.66 82.17 REMARK 500 ASN A 246 -167.80 -169.68 REMARK 500 SER A 249 56.81 -98.10 REMARK 500 TYR A 253 154.24 -47.13 REMARK 500 ALA A 342 61.67 -152.86 REMARK 500 PHE A 356 -76.34 -154.29 REMARK 500 ALA A 385 58.55 -114.19 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 NA A2005 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 57 O REMARK 620 2 HIS A 70 ND1 83.8 REMARK 620 3 HOH A2089 O 113.8 101.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A2004 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 162 OD1 REMARK 620 2 ARG A 207 N 108.3 REMARK 620 3 TYR A 211 OH 111.9 132.6 REMARK 620 4 HOH A2319 O 104.5 101.6 91.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A2001 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 180 OE2 REMARK 620 2 GLU A 216 OE1 94.3 REMARK 620 3 ASP A 244 OD2 92.6 111.7 REMARK 620 4 ASP A 286 OD2 162.4 83.7 104.4 REMARK 620 5 ASP A 286 OD2 150.2 113.0 88.4 29.7 REMARK 620 6 GLC A1001 O4 85.0 164.0 84.3 92.1 65.4 REMARK 620 7 GLC A1001 O3 84.6 90.3 158.0 77.9 83.5 73.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A2002 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 216 OE2 REMARK 620 2 HIS A 219 NE2 80.7 REMARK 620 3 ASP A 254 OD2 157.0 91.5 REMARK 620 4 ASP A 254 OD1 100.2 89.4 57.8 REMARK 620 5 ASP A 256 OD1 89.6 167.1 94.2 83.9 REMARK 620 6 HOH A2416 O 113.0 106.9 89.9 144.7 84.7 REMARK 620 N 1 2 3 4 5 REMARK 999 REMARK 999 ACCORDING TO THE AUTHOR, THE SWISS-PROT REMARK 999 SEQUENCE (ACCESSION P15587)CONTAINS AN REMARK 999 ERROR AT POSITION 175. THR175 SHOULD BE ILE175, REMARK 999 HOWEVER, THE CONFLICT IS NOT YET NOTED IN REMARK 999 SWISS-PROT ENTRY P15587. DBREF 1S5M A 1 386 UNP P15587 XYLA_STROL 1 386 SEQADV 1S5M 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 GLC A1001 24 HET MN A2001 1 HET MN A2002 1 HET NA A2004 1 HET NA A2005 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC C6 H12 O6 FORMUL 3 MN 2(MN 2+) FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *411(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 NA NA A2005 1555 1555 2.69 LINK ND1 HIS A 70 NA NA A2005 1555 1555 2.88 LINK OD1 ASP A 162 NA NA A2004 1555 1555 2.70 LINK OE2 GLU A 180 MN MN A2001 1555 1555 2.10 LINK N ARG A 207 NA NA A2004 1555 1555 2.95 LINK OH TYR A 211 NA NA A2004 1555 1555 2.76 LINK OE1 GLU A 216 MN MN A2001 1555 1555 2.04 LINK OE2 GLU A 216 MN MN A2002 1555 1555 2.05 LINK NE2 HIS A 219 MN MN A2002 1555 1555 2.31 LINK OD2 ASP A 244 MN MN A2001 1555 1555 2.15 LINK OD2 ASP A 254 MN MN A2002 1555 1555 2.22 LINK OD1 ASP A 254 MN MN A2002 1555 1555 2.30 LINK OD1 ASP A 256 MN MN A2002 1555 1555 2.20 LINK OD2AASP A 286 MN MN A2001 1555 1555 2.13 LINK OD2BASP A 286 MN MN A2001 1555 1555 2.17 LINK O4 GLC A1001 MN MN A2001 1555 1555 2.25 LINK O3 GLC A1001 MN MN A2001 1555 1555 2.40 LINK MN MN A2002 O HOH A2416 1555 1555 2.17 LINK NA NA A2004 O HOH A2319 1555 1555 2.82 LINK NA NA A2005 O HOH A2089 1555 1555 2.73 CISPEP 1 GLU A 185 PRO A 186 0 19.92 CRYST1 85.865 92.968 98.298 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 0.011646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010756 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010173 0.00000