HEADER ISOMERASE 23-MAR-10 3M9Y TITLE CRYSTAL STRUCTURE OF TRIOSEPHOSPHATE ISOMERASE FROM METHICILLIN TITLE 2 RESISTANT STAPHYLOCOCCUS AUREUS AT 1.9 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIOSEPHOSPHATE ISOMERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TIM, TRIOSE-PHOSPHATE ISOMERASE; COMPND 5 EC: 5.3.1.1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS; SOURCE 3 ORGANISM_TAXID: 282458; SOURCE 4 STRAIN: MRSA252; SOURCE 5 GENE: SAR0830, TPI, TPIA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE30 KEYWDS TIM BARREL, GLYCOLYSIS, GLUCONEOGENESIS, ISOMERASE, PENTOSE SHUNT EXPDTA X-RAY DIFFRACTION AUTHOR S.MUKHERJEE,D.DUTTA,B.SAHA,A.K.DAS REVDAT 5 01-NOV-23 3M9Y 1 REMARK SEQADV LINK REVDAT 4 26-JUN-13 3M9Y 1 JRNL REVDAT 3 17-OCT-12 3M9Y 1 JRNL VERSN REMARK REVDAT 2 13-APR-11 3M9Y 1 ATOM REVDAT 1 06-APR-11 3M9Y 0 JRNL AUTH S.MUKHERJEE,A.ROYCHOWDHURY,D.DUTTA,A.K.DAS JRNL TITL CRYSTAL STRUCTURES OF TRIOSEPHOSPHATE ISOMERASE FROM JRNL TITL 2 METHICILLIN RESISTANT STAPHYLOCOCCUS AUREUS MRSA252 PROVIDE JRNL TITL 3 STRUCTURAL INSIGHTS INTO NOVEL MODES OF LIGAND BINDING AND JRNL TITL 4 UNIQUE CONFORMATIONS OF CATALYTIC LOOP JRNL REF BIOCHIMIE V. 94 2532 2012 JRNL REFN ISSN 0300-9084 JRNL PMID 22813930 JRNL DOI 10.1016/J.BIOCHI.2012.07.001 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 44825 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2258 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2972 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE SET COUNT : 171 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3825 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 481 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.10000 REMARK 3 B22 (A**2) : 1.10000 REMARK 3 B33 (A**2) : -2.21000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.128 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.127 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.189 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3916 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5298 ; 1.842 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 511 ; 5.822 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 171 ;38.137 ;26.374 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 702 ;13.790 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;11.336 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 608 ; 0.150 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2923 ; 0.010 ; 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): 2514 ; 1.275 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4043 ; 2.174 ; 2.500 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1402 ; 5.316 ; 5.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1251 ; 8.335 ;10.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 3 A 107 2 REMARK 3 1 B 3 B 107 2 REMARK 3 2 A 110 A 156 2 REMARK 3 2 B 110 B 156 2 REMARK 3 3 A 160 A 172 2 REMARK 3 3 B 160 B 172 2 REMARK 3 4 A 186 A 242 2 REMARK 3 4 B 186 B 242 2 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT POSITIONAL 1 A (A): 884 ; 0.100 ; 0.050 REMARK 3 MEDIUM POSITIONAL 1 A (A): 776 ; 0.130 ; 0.500 REMARK 3 TIGHT THERMAL 1 A (A**2): 884 ; 1.210 ; 1.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 776 ; 1.450 ; 2.500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 0 A 253 REMARK 3 ORIGIN FOR THE GROUP (A): 56.2495 13.0326 -8.0317 REMARK 3 T TENSOR REMARK 3 T11: 0.0272 T22: 0.1290 REMARK 3 T33: 0.0744 T12: -0.0176 REMARK 3 T13: 0.0360 T23: -0.0065 REMARK 3 L TENSOR REMARK 3 L11: 1.5165 L22: 0.5929 REMARK 3 L33: 1.3815 L12: -0.0339 REMARK 3 L13: 0.0149 L23: 0.2821 REMARK 3 S TENSOR REMARK 3 S11: 0.0338 S12: 0.2816 S13: 0.1546 REMARK 3 S21: -0.1188 S22: 0.0555 S23: -0.1667 REMARK 3 S31: -0.1101 S32: 0.2647 S33: -0.0893 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 0 B 253 REMARK 3 ORIGIN FOR THE GROUP (A): 34.7112 19.6611 17.4992 REMARK 3 T TENSOR REMARK 3 T11: 0.0125 T22: 0.0251 REMARK 3 T33: 0.0429 T12: 0.0053 REMARK 3 T13: -0.0055 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 0.6811 L22: 0.9265 REMARK 3 L33: 2.0168 L12: -0.1842 REMARK 3 L13: 0.1097 L23: 0.5453 REMARK 3 S TENSOR REMARK 3 S11: -0.0207 S12: -0.0670 S13: 0.0931 REMARK 3 S21: 0.0033 S22: -0.0201 S23: 0.0436 REMARK 3 S31: -0.1309 S32: -0.1127 S33: 0.0408 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: U VALUES: RESIDUAL ONLY REMARK 4 REMARK 4 3M9Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : VARIMAX MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.9 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44961 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 72.365 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 12.10 REMARK 200 R MERGE FOR SHELL (I) : 0.43300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2BTM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6M TRISODIUM CITRATE DIHYDRATE, PH REMARK 280 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 87.50300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.73900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.73900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 131.25450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.73900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.73900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.75150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.73900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.73900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 131.25450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.73900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.73900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 43.75150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 87.50300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 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 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 THR A 176 REMARK 465 GLY A 177 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 CG GLU B 250 O HOH B 342 2.16 REMARK 500 CE LYS B 120 O HOH B 511 2.16 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 21 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 GLY B 175 N - CA - C ANGL. DEV. = -16.0 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 LYS A 11 -149.31 53.91 REMARK 500 LYS A 14 141.78 87.85 REMARK 500 SER A 200 -99.18 -144.97 REMARK 500 LYS B 11 -139.61 53.75 REMARK 500 MET B 12 76.51 -101.19 REMARK 500 LYS B 14 145.60 83.54 REMARK 500 THR B 176 138.48 73.40 REMARK 500 SER B 200 -99.87 -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 NA B 254 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 225 O REMARK 620 2 GLN B 227 O 98.1 REMARK 620 3 ILE B 230 O 105.3 95.4 REMARK 620 4 HOH B 305 O 87.3 171.6 89.3 REMARK 620 5 HOH B 327 O 89.7 87.3 164.2 86.4 REMARK 620 6 HOH B 359 O 167.8 90.2 82.7 83.5 81.7 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 254 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 255 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CIT B 256 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UWU RELATED DB: PDB REMARK 900 RELATED ID: 3UWV RELATED DB: PDB REMARK 900 RELATED ID: 3UWW RELATED DB: PDB REMARK 900 RELATED ID: 3UWY RELATED DB: PDB REMARK 900 RELATED ID: 3UWZ RELATED DB: PDB DBREF 3M9Y A 1 253 UNP Q6GIL6 TPIS_STAAR 1 253 DBREF 3M9Y B 1 253 UNP Q6GIL6 TPIS_STAAR 1 253 SEQADV 3M9Y SER A 0 UNP Q6GIL6 EXPRESSION TAG SEQADV 3M9Y SER B 0 UNP Q6GIL6 EXPRESSION TAG SEQRES 1 A 254 SER MET ARG THR PRO ILE ILE ALA GLY ASN TRP LYS MET SEQRES 2 A 254 ASN LYS THR VAL GLN GLU ALA LYS ASP PHE VAL ASN ALA SEQRES 3 A 254 LEU PRO THR LEU PRO ASP SER LYS GLU VAL GLU SER VAL SEQRES 4 A 254 ILE CYS ALA PRO ALA ILE GLN LEU ASP ALA LEU THR THR SEQRES 5 A 254 ALA VAL LYS GLU GLY LYS ALA GLN GLY LEU GLU ILE GLY SEQRES 6 A 254 ALA GLN ASN THR TYR PHE GLU ASP ASN GLY ALA PHE THR SEQRES 7 A 254 GLY GLU THR SER PRO VAL ALA LEU ALA ASP LEU GLY VAL SEQRES 8 A 254 LYS TYR VAL VAL ILE GLY HIS SER GLU ARG ARG GLU LEU SEQRES 9 A 254 PHE HIS GLU THR ASP GLU GLU ILE ASN LYS LYS ALA HIS SEQRES 10 A 254 ALA ILE PHE LYS HIS GLY MET THR PRO ILE ILE CYS VAL SEQRES 11 A 254 GLY GLU THR ASP GLU GLU ARG GLU SER GLY LYS ALA ASN SEQRES 12 A 254 ASP VAL VAL GLY GLU GLN VAL LYS LYS ALA VAL ALA GLY SEQRES 13 A 254 LEU SER GLU ASP GLN LEU LYS SER VAL VAL ILE ALA TYR SEQRES 14 A 254 GLU PRO ILE TRP ALA ILE GLY THR GLY LYS SER SER THR SEQRES 15 A 254 SER GLU ASP ALA ASN GLU MET CYS ALA PHE VAL ARG GLN SEQRES 16 A 254 THR ILE ALA ASP LEU SER SER LYS GLU VAL SER GLU ALA SEQRES 17 A 254 THR ARG ILE GLN TYR GLY GLY SER VAL LYS PRO ASN ASN SEQRES 18 A 254 ILE LYS GLU TYR MET ALA GLN THR ASP ILE ASP GLY ALA SEQRES 19 A 254 LEU VAL GLY GLY ALA SER LEU LYS VAL GLU ASP PHE VAL SEQRES 20 A 254 GLN LEU LEU GLU GLY ALA LYS SEQRES 1 B 254 SER MET ARG THR PRO ILE ILE ALA GLY ASN TRP LYS MET SEQRES 2 B 254 ASN LYS THR VAL GLN GLU ALA LYS ASP PHE VAL ASN ALA SEQRES 3 B 254 LEU PRO THR LEU PRO ASP SER LYS GLU VAL GLU SER VAL SEQRES 4 B 254 ILE CYS ALA PRO ALA ILE GLN LEU ASP ALA LEU THR THR SEQRES 5 B 254 ALA VAL LYS GLU GLY LYS ALA GLN GLY LEU GLU ILE GLY SEQRES 6 B 254 ALA GLN ASN THR TYR PHE GLU ASP ASN GLY ALA PHE THR SEQRES 7 B 254 GLY GLU THR SER PRO VAL ALA LEU ALA ASP LEU GLY VAL SEQRES 8 B 254 LYS TYR VAL VAL ILE GLY HIS SER GLU ARG ARG GLU LEU SEQRES 9 B 254 PHE HIS GLU THR ASP GLU GLU ILE ASN LYS LYS ALA HIS SEQRES 10 B 254 ALA ILE PHE LYS HIS GLY MET THR PRO ILE ILE CYS VAL SEQRES 11 B 254 GLY GLU THR ASP GLU GLU ARG GLU SER GLY LYS ALA ASN SEQRES 12 B 254 ASP VAL VAL GLY GLU GLN VAL LYS LYS ALA VAL ALA GLY SEQRES 13 B 254 LEU SER GLU ASP GLN LEU LYS SER VAL VAL ILE ALA TYR SEQRES 14 B 254 GLU PRO ILE TRP ALA ILE GLY THR GLY LYS SER SER THR SEQRES 15 B 254 SER GLU ASP ALA ASN GLU MET CYS ALA PHE VAL ARG GLN SEQRES 16 B 254 THR ILE ALA ASP LEU SER SER LYS GLU VAL SER GLU ALA SEQRES 17 B 254 THR ARG ILE GLN TYR GLY GLY SER VAL LYS PRO ASN ASN SEQRES 18 B 254 ILE LYS GLU TYR MET ALA GLN THR ASP ILE ASP GLY ALA SEQRES 19 B 254 LEU VAL GLY GLY ALA SER LEU LYS VAL GLU ASP PHE VAL SEQRES 20 B 254 GLN LEU LEU GLU GLY ALA LYS HET NA B 254 1 HET NA B 255 1 HET CIT B 256 13 HETNAM NA SODIUM ION HETNAM CIT CITRIC ACID FORMUL 3 NA 2(NA 1+) FORMUL 5 CIT C6 H8 O7 FORMUL 6 HOH *481(H2 O) HELIX 1 1 THR A 15 LEU A 26 1 12 HELIX 2 2 PRO A 42 ILE A 44 5 3 HELIX 3 3 GLN A 45 GLU A 55 1 11 HELIX 4 4 SER A 81 LEU A 88 1 8 HELIX 5 5 HIS A 97 PHE A 104 1 8 HELIX 6 6 THR A 107 HIS A 121 1 15 HELIX 7 7 THR A 132 SER A 138 1 7 HELIX 8 8 LYS A 140 ALA A 154 1 15 HELIX 9 9 SER A 157 VAL A 164 1 8 HELIX 10 10 PRO A 170 ILE A 174 5 5 HELIX 11 11 THR A 181 SER A 200 1 20 HELIX 12 12 SER A 201 GLU A 206 1 6 HELIX 13 13 ASN A 220 ALA A 226 1 7 HELIX 14 14 GLY A 236 LEU A 240 5 5 HELIX 15 15 LYS A 241 LYS A 253 1 13 HELIX 16 16 THR B 15 LEU B 26 1 12 HELIX 17 17 PRO B 42 ILE B 44 5 3 HELIX 18 18 GLN B 45 GLU B 55 1 11 HELIX 19 19 SER B 81 LEU B 88 1 8 HELIX 20 20 HIS B 97 PHE B 104 1 8 HELIX 21 21 THR B 107 HIS B 121 1 15 HELIX 22 22 THR B 132 SER B 138 1 7 HELIX 23 23 LYS B 140 VAL B 153 1 14 HELIX 24 24 SER B 157 VAL B 164 1 8 HELIX 25 25 PRO B 170 ILE B 174 5 5 HELIX 26 26 THR B 181 SER B 200 1 20 HELIX 27 27 SER B 201 GLU B 206 1 6 HELIX 28 28 ASN B 220 ALA B 226 1 7 HELIX 29 29 GLY B 236 LEU B 240 5 5 HELIX 30 30 LYS B 241 GLY B 251 1 11 SHEET 1 A 9 ILE A 5 ASN A 9 0 SHEET 2 A 9 GLU A 36 ALA A 41 1 O VAL A 38 N GLY A 8 SHEET 3 A 9 GLU A 62 ALA A 65 1 O GLY A 64 N ILE A 39 SHEET 4 A 9 TYR A 92 ILE A 95 1 O VAL A 94 N ALA A 65 SHEET 5 A 9 THR A 124 VAL A 129 1 O CYS A 128 N ILE A 95 SHEET 6 A 9 VAL A 165 TYR A 168 1 O VAL A 165 N ILE A 127 SHEET 7 A 9 ARG A 209 TYR A 212 1 O GLN A 211 N TYR A 168 SHEET 8 A 9 GLY A 232 VAL A 235 1 O GLY A 232 N TYR A 212 SHEET 9 A 9 ILE A 5 ASN A 9 1 N ASN A 9 O VAL A 235 SHEET 1 B 9 ILE B 5 ASN B 9 0 SHEET 2 B 9 GLU B 36 CYS B 40 1 O CYS B 40 N GLY B 8 SHEET 3 B 9 GLU B 62 ALA B 65 1 O GLY B 64 N ILE B 39 SHEET 4 B 9 TYR B 92 ILE B 95 1 O VAL B 94 N ALA B 65 SHEET 5 B 9 THR B 124 VAL B 129 1 O ILE B 126 N ILE B 95 SHEET 6 B 9 VAL B 165 TYR B 168 1 O VAL B 165 N ILE B 127 SHEET 7 B 9 ARG B 209 TYR B 212 1 O GLN B 211 N ILE B 166 SHEET 8 B 9 GLY B 232 VAL B 235 1 O GLY B 232 N TYR B 212 SHEET 9 B 9 ILE B 5 ASN B 9 1 N ASN B 9 O VAL B 235 LINK OG1 THR A 80 NA NA B 255 1555 1555 2.82 LINK O MET B 225 NA NA B 254 1555 1555 2.28 LINK O GLN B 227 NA NA B 254 1555 1555 2.54 LINK O ILE B 230 NA NA B 254 1555 1555 2.42 LINK NA NA B 254 O HOH B 305 1555 1555 2.42 LINK NA NA B 254 O HOH B 327 1555 1555 2.43 LINK NA NA B 254 O HOH B 359 1555 1555 2.58 SITE 1 AC1 6 MET B 225 GLN B 227 ILE B 230 HOH B 305 SITE 2 AC1 6 HOH B 327 HOH B 359 SITE 1 AC2 4 THR A 80 PRO B 42 ALA B 43 ILE B 44 SITE 1 AC3 12 LYS B 11 SER B 215 LYS B 217 GLY B 236 SITE 2 AC3 12 GLY B 237 HOH B 285 HOH B 301 HOH B 306 SITE 3 AC3 12 HOH B 354 HOH B 355 HOH B 365 HOH B 475 CRYST1 79.478 79.478 175.006 90.00 90.00 90.00 P 43 21 2 16 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 0.012582 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005714 0.00000