HEADER ISOMERASE 20-MAR-15 4YWI TITLE F96S/L167V DOUBLE MUTANT OF PLASMODIUM FALCIPARUM TRIOSEPHOSPHATE TITLE 2 ISOMERASE 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; COMPND 7 MUTATION: YES; COMPND 8 OTHER_DETAILS: MUTATION OF A163V PRESENT IN THE WILD TYPE TIM COMPND 9 CONSIDERED AS TEMPLATE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM FALCIPARUM; SOURCE 3 ORGANISM_TAXID: 5833; SOURCE 4 GENE: TPI; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: AA200; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRC99A KEYWDS TIM BARRELS, BETA-ALPHA BARRELS, ISOMERASE, GLYCOLYSIS EXPDTA X-RAY DIFFRACTION AUTHOR V.PAREEK,P.BALARAM,M.R.N.MURTHY REVDAT 3 08-NOV-23 4YWI 1 REMARK REVDAT 2 20-APR-16 4YWI 1 JRNL REVDAT 1 03-FEB-16 4YWI 0 JRNL AUTH V.PAREEK,M.SAMANTA,N.V.JOSHI,H.BALARAM,M.R.N.MURTHY, JRNL AUTH 2 P.BALARAM JRNL TITL CONNECTING ACTIVE-SITE LOOP CONFORMATIONS AND CATALYSIS IN JRNL TITL 2 TRIOSEPHOSPHATE ISOMERASE: INSIGHTS FROM A RARE VARIATION AT JRNL TITL 3 RESIDUE 96 IN THE PLASMODIAL ENZYME JRNL REF CHEMBIOCHEM V. 17 620 2016 JRNL REFN ESSN 1439-7633 JRNL PMID 26762569 JRNL DOI 10.1002/CBIC.201500532 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 83.6 REMARK 3 NUMBER OF REFLECTIONS : 32800 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1759 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1366 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 47.51 REMARK 3 BIN R VALUE (WORKING SET) : 0.2140 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3836 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 38 REMARK 3 SOLVENT ATOMS : 421 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.05000 REMARK 3 B33 (A**2) : -0.07000 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): 0.036 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.031 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.600 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3950 ; 0.008 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3753 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5324 ; 1.248 ; 1.947 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8626 ; 0.760 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 493 ; 5.968 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 185 ;38.041 ;25.459 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 697 ;12.679 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 16 ;14.683 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 611 ; 0.071 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4486 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 898 ; 0.001 ; 0.020 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): 1971 ; 0.966 ; 1.921 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1970 ; 0.964 ; 1.920 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2456 ; 1.557 ; 2.866 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2457 ; 1.558 ; 2.866 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1979 ; 1.236 ; 2.046 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1979 ; 1.235 ; 2.046 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2866 ; 1.969 ; 3.008 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4830 ; 3.707 ;15.896 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4655 ; 3.423 ;15.532 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 : 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 4YWI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 ULTRAX 18 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35109 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.6 REMARK 200 DATA REDUNDANCY : 2.300 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 38.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 61.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.10 REMARK 200 R MERGE FOR SHELL (I) : 0.18000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 12.80 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1M7P REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 1450 22%, HEPES, LI2SO4 10MM, DTT REMARK 280 0.5MM, NAN3 0.5MM, EDTA 0.5MM, PH 8.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-Y,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 25.46650 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 87.24750 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 25.46650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 87.24750 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: 5150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -33.0 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 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 B 548 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 573 LIES ON A SPECIAL POSITION. 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 171 REMARK 465 MET B 1 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 LYS A 53 CD CE NZ REMARK 470 LYS A 84 CE NZ REMARK 470 LYS A 100 NZ REMARK 470 GLU A 107 OE1 OE2 REMARK 470 LYS A 118 CD CE NZ REMARK 470 LYS A 138 NZ REMARK 470 LYS A 145 CE NZ REMARK 470 ILE A 170 CG2 CD1 REMARK 470 THR A 172 N CG2 REMARK 470 GLY A 173 CA C O REMARK 470 LYS A 174 N CA CB CG CD CE NZ REMARK 470 THR A 175 CG2 REMARK 470 LYS A 186 CD CE NZ REMARK 470 ASP A 194 OD1 OD2 REMARK 470 LYS A 199 CD CE NZ REMARK 470 GLU A 224 OE1 OE2 REMARK 470 ALA B 2 CB REMARK 470 LYS B 21 CE NZ REMARK 470 GLU B 107 OE1 REMARK 470 GLN B 114 NE2 REMARK 470 ASN B 137 OD1 ND2 REMARK 470 ILE B 140 CD1 REMARK 470 ASP B 155 CG OD1 OD2 REMARK 470 ILE B 170 CG2 CD1 REMARK 470 THR B 172 N OG1 REMARK 470 GLY B 173 N CA REMARK 470 LYS B 174 O CB CG CD CE NZ REMARK 470 LYS B 193 NZ REMARK 470 LYS B 199 CD CE NZ REMARK 470 GLU B 215 OE1 OE2 REMARK 470 GLN B 222 CG CD OE1 NE2 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 O1 EDO A 302 O HOH A 401 1.33 REMARK 500 OE2 GLU A 135 O HOH A 402 1.92 REMARK 500 O HOH A 404 O HOH A 466 2.18 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 GLU A 77 CD GLU A 77 OE1 -0.068 REMARK 500 GLU A 215 CD GLU A 215 OE2 -0.073 REMARK 500 GLU B 89 CD GLU B 89 OE2 -0.068 REMARK 500 GLU B 165 CD GLU B 165 OE1 -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 ASP A 49 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG B 3 NE - CZ - NH2 ANGL. DEV. = -3.8 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 12 -146.45 55.43 REMARK 500 LYS B 12 -146.85 53.37 REMARK 500 LYS B 174 88.54 94.25 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE B 170 GLY B 171 -136.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 305 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4YXG RELATED DB: PDB REMARK 900 RELATED ID: 4Z0J RELATED DB: PDB REMARK 900 RELATED ID: 4Z0S RELATED DB: PDB DBREF 4YWI A 1 248 UNP Q07412 TPIS_PLAFA 1 248 DBREF 4YWI B 1 248 UNP Q07412 TPIS_PLAFA 1 248 SEQADV 4YWI SER A 96 UNP Q07412 PHE 96 ENGINEERED MUTATION SEQADV 4YWI VAL A 163 UNP Q07412 ALA 163 ENGINEERED MUTATION SEQADV 4YWI VAL A 167 UNP Q07412 LEU 167 ENGINEERED MUTATION SEQADV 4YWI SER B 96 UNP Q07412 PHE 96 ENGINEERED MUTATION SEQADV 4YWI VAL B 163 UNP Q07412 ALA 163 ENGINEERED MUTATION SEQADV 4YWI VAL B 167 UNP Q07412 LEU 167 ENGINEERED MUTATION SEQRES 1 A 248 MET ALA ARG LYS TYR PHE VAL ALA ALA ASN TRP LYS CYS SEQRES 2 A 248 ASN GLY THR LEU GLU SER ILE LYS SER LEU THR ASN SER SEQRES 3 A 248 PHE ASN ASN LEU ASP PHE ASP PRO SER LYS LEU ASP VAL SEQRES 4 A 248 VAL VAL PHE PRO VAL SER VAL HIS TYR ASP HIS THR ARG SEQRES 5 A 248 LYS LEU LEU GLN SER LYS PHE SER THR GLY ILE GLN ASN SEQRES 6 A 248 VAL SER LYS PHE GLY ASN GLY SER TYR THR GLY GLU VAL SEQRES 7 A 248 SER ALA GLU ILE ALA LYS ASP LEU ASN ILE GLU TYR VAL SEQRES 8 A 248 ILE ILE GLY HIS SER GLU ARG ARG LYS TYR PHE HIS GLU SEQRES 9 A 248 THR ASP GLU ASP VAL ARG GLU LYS LEU GLN ALA SER LEU SEQRES 10 A 248 LYS ASN ASN LEU LYS ALA VAL VAL CYS PHE GLY GLU SER SEQRES 11 A 248 LEU GLU GLN ARG GLU GLN ASN LYS THR ILE GLU VAL ILE SEQRES 12 A 248 THR LYS GLN VAL LYS ALA PHE VAL ASP LEU ILE ASP ASN SEQRES 13 A 248 PHE ASP ASN VAL ILE LEU VAL TYR GLU PRO VAL TRP ALA SEQRES 14 A 248 ILE GLY THR GLY LYS THR ALA THR PRO GLU GLN ALA GLN SEQRES 15 A 248 LEU VAL HIS LYS GLU ILE ARG LYS ILE VAL LYS ASP THR SEQRES 16 A 248 CYS GLY GLU LYS GLN ALA ASN GLN ILE ARG ILE LEU TYR SEQRES 17 A 248 GLY GLY SER VAL ASN THR GLU ASN CYS SER SER LEU ILE SEQRES 18 A 248 GLN GLN GLU ASP ILE ASP GLY PHE LEU VAL GLY ASN ALA SEQRES 19 A 248 SER LEU LYS GLU SER PHE VAL ASP ILE ILE LYS SER ALA SEQRES 20 A 248 MET SEQRES 1 B 248 MET ALA ARG LYS TYR PHE VAL ALA ALA ASN TRP LYS CYS SEQRES 2 B 248 ASN GLY THR LEU GLU SER ILE LYS SER LEU THR ASN SER SEQRES 3 B 248 PHE ASN ASN LEU ASP PHE ASP PRO SER LYS LEU ASP VAL SEQRES 4 B 248 VAL VAL PHE PRO VAL SER VAL HIS TYR ASP HIS THR ARG SEQRES 5 B 248 LYS LEU LEU GLN SER LYS PHE SER THR GLY ILE GLN ASN SEQRES 6 B 248 VAL SER LYS PHE GLY ASN GLY SER TYR THR GLY GLU VAL SEQRES 7 B 248 SER ALA GLU ILE ALA LYS ASP LEU ASN ILE GLU TYR VAL SEQRES 8 B 248 ILE ILE GLY HIS SER GLU ARG ARG LYS TYR PHE HIS GLU SEQRES 9 B 248 THR ASP GLU ASP VAL ARG GLU LYS LEU GLN ALA SER LEU SEQRES 10 B 248 LYS ASN ASN LEU LYS ALA VAL VAL CYS PHE GLY GLU SER SEQRES 11 B 248 LEU GLU GLN ARG GLU GLN ASN LYS THR ILE GLU VAL ILE SEQRES 12 B 248 THR LYS GLN VAL LYS ALA PHE VAL ASP LEU ILE ASP ASN SEQRES 13 B 248 PHE ASP ASN VAL ILE LEU VAL TYR GLU PRO VAL TRP ALA SEQRES 14 B 248 ILE GLY THR GLY LYS THR ALA THR PRO GLU GLN ALA GLN SEQRES 15 B 248 LEU VAL HIS LYS GLU ILE ARG LYS ILE VAL LYS ASP THR SEQRES 16 B 248 CYS GLY GLU LYS GLN ALA ASN GLN ILE ARG ILE LEU TYR SEQRES 17 B 248 GLY GLY SER VAL ASN THR GLU ASN CYS SER SER LEU ILE SEQRES 18 B 248 GLN GLN GLU ASP ILE ASP GLY PHE LEU VAL GLY ASN ALA SEQRES 19 B 248 SER LEU LYS GLU SER PHE VAL ASP ILE ILE LYS SER ALA SEQRES 20 B 248 MET HET SO4 A 301 5 HET EDO A 302 4 HET EDO A 303 4 HET EDO A 304 4 HET SO4 B 301 5 HET EDO B 302 4 HET EDO B 303 4 HET EDO B 304 4 HET EDO B 305 4 HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 SO4 2(O4 S 2-) FORMUL 4 EDO 7(C2 H6 O2) FORMUL 12 HOH *421(H2 O) HELIX 1 AA1 THR A 16 ASN A 29 1 14 HELIX 2 AA2 VAL A 44 VAL A 46 5 3 HELIX 3 AA3 HIS A 47 LEU A 55 1 9 HELIX 4 AA4 SER A 79 LEU A 86 1 8 HELIX 5 AA5 HIS A 95 HIS A 103 1 9 HELIX 6 AA6 THR A 105 ASN A 119 1 15 HELIX 7 AA7 SER A 130 GLN A 136 1 7 HELIX 8 AA8 LYS A 138 ALA A 149 1 12 HELIX 9 AA9 PHE A 150 ILE A 154 5 5 HELIX 10 AB1 PRO A 166 ILE A 170 5 5 HELIX 11 AB2 THR A 177 GLY A 197 1 21 HELIX 12 AB3 GLY A 197 ILE A 204 1 8 HELIX 13 AB4 ASN A 216 GLN A 222 1 7 HELIX 14 AB5 GLY A 232 GLU A 238 5 7 HELIX 15 AB6 SER A 239 SER A 246 1 8 HELIX 16 AB7 THR B 16 ASN B 29 1 14 HELIX 17 AB8 VAL B 44 VAL B 46 5 3 HELIX 18 AB9 HIS B 47 LEU B 55 1 9 HELIX 19 AC1 SER B 79 LEU B 86 1 8 HELIX 20 AC2 HIS B 95 PHE B 102 1 8 HELIX 21 AC3 THR B 105 ASN B 119 1 15 HELIX 22 AC4 SER B 130 GLN B 136 1 7 HELIX 23 AC5 LYS B 138 ALA B 149 1 12 HELIX 24 AC6 PHE B 150 ILE B 154 5 5 HELIX 25 AC7 PRO B 166 ILE B 170 5 5 HELIX 26 AC8 THR B 177 CYS B 196 1 20 HELIX 27 AC9 GLY B 197 ILE B 204 1 8 HELIX 28 AD1 ASN B 216 GLN B 222 1 7 HELIX 29 AD2 GLY B 232 GLU B 238 5 7 HELIX 30 AD3 SER B 239 SER B 246 1 8 SHEET 1 AA1 9 PHE A 6 ASN A 10 0 SHEET 2 AA1 9 ASP A 38 PHE A 42 1 O VAL A 40 N ALA A 9 SHEET 3 AA1 9 SER A 60 ILE A 63 1 O SER A 60 N VAL A 39 SHEET 4 AA1 9 TYR A 90 ILE A 93 1 O TYR A 90 N ILE A 63 SHEET 5 AA1 9 LYS A 122 PHE A 127 1 O CYS A 126 N ILE A 93 SHEET 6 AA1 9 VAL A 160 TYR A 164 1 O ILE A 161 N ALA A 123 SHEET 7 AA1 9 ILE A 206 TYR A 208 1 O LEU A 207 N LEU A 162 SHEET 8 AA1 9 GLY A 228 VAL A 231 1 O GLY A 228 N TYR A 208 SHEET 9 AA1 9 PHE A 6 ASN A 10 1 N ALA A 8 O VAL A 231 SHEET 1 AA2 9 PHE B 6 ASN B 10 0 SHEET 2 AA2 9 ASP B 38 PHE B 42 1 O PHE B 42 N ALA B 9 SHEET 3 AA2 9 SER B 60 ILE B 63 1 O SER B 60 N VAL B 39 SHEET 4 AA2 9 TYR B 90 ILE B 93 1 O TYR B 90 N ILE B 63 SHEET 5 AA2 9 LYS B 122 PHE B 127 1 O VAL B 124 N VAL B 91 SHEET 6 AA2 9 VAL B 160 TYR B 164 1 O ILE B 161 N ALA B 123 SHEET 7 AA2 9 ILE B 206 TYR B 208 1 O LEU B 207 N LEU B 162 SHEET 8 AA2 9 GLY B 228 VAL B 231 1 O GLY B 228 N TYR B 208 SHEET 9 AA2 9 PHE B 6 ASN B 10 1 N ASN B 10 O VAL B 231 CISPEP 1 LYS B 174 THR B 175 0 15.81 SITE 1 AC1 6 SER A 211 ASN A 233 HOH A 426 HOH A 434 SITE 2 AC1 6 HOH A 460 HOH A 494 SITE 1 AC2 5 ARG A 134 ILE A 140 ASP A 152 HOH A 401 SITE 2 AC2 5 HOH A 471 SITE 1 AC3 5 SER A 19 SER A 22 LEU A 23 GLU A 238 SITE 2 AC3 5 HOH A 483 SITE 1 AC4 7 ASN A 65 VAL A 78 HOH A 417 HOH A 495 SITE 2 AC4 7 HOH A 497 HOH A 553 GLY B 76 SITE 1 AC5 7 SER B 211 GLY B 232 ASN B 233 EDO B 303 SITE 2 AC5 7 HOH B 415 HOH B 420 HOH B 464 SITE 1 AC6 7 GLY A 76 HOH A 452 HOH A 553 SER B 45 SITE 2 AC6 7 ASN B 65 HOH B 409 HOH B 417 SITE 1 AC7 8 ASN B 10 LYS B 12 HIS B 95 LEU B 230 SITE 2 AC7 8 GLY B 232 SO4 B 301 HOH B 402 HOH B 479 SITE 1 AC8 3 SER A 246 GLU B 179 HOH B 515 SITE 1 AC9 7 TRP B 11 ASN B 14 GLY B 15 SER B 19 SITE 2 AC9 7 ILE B 20 LEU B 236 HOH B 407 CRYST1 50.933 53.809 174.495 90.00 90.00 90.00 P 21 2 21 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 0.019634 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018584 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005731 0.00000