HEADER ISOMERASE 08-MAR-15 4YMZ TITLE DHAP BOUND LEPTOSPIRA INTERROGANS TRIOSEPHOSPHATE ISOMERASE (LITIM) 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: LEPTOSPIRA INTERROGANS SEROVAR SOURCE 3 ICTEROHAEMORRHAGIAE STR. RGA; SOURCE 4 ORGANISM_TAXID: 1291351; SOURCE 5 STRAIN: RGA; SOURCE 6 GENE: LEP2GSC113_RS0110880; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: AA200; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PTRC99A KEYWDS TIM BARRELS, BETA-ALPHA BARRELS, ISOMERASE, DIHYDROXYACETONE KEYWDS 2 PHOSPHATE, GLYCOLYSIS EXPDTA X-RAY DIFFRACTION AUTHOR V.PAREEK,P.BALARAM,M.R.N.MURTHY REVDAT 3 08-NOV-23 4YMZ 1 REMARK REVDAT 2 20-APR-16 4YMZ 1 JRNL REVDAT 1 09-MAR-16 4YMZ 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. 1.87 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) : 1.87 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 52007 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 2593 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) : 1.87 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3098 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 75.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE SET COUNT : 184 REMARK 3 BIN FREE R VALUE : 0.2230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3739 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 90 REMARK 3 SOLVENT ATOMS : 306 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.114 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.116 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.070 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.278 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3898 ; 0.021 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3701 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5241 ; 2.015 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8508 ; 0.942 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 505 ; 6.229 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 147 ;34.676 ;24.558 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 649 ;12.606 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;13.870 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 604 ; 0.131 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4379 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 856 ; 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): 2014 ; 2.578 ; 2.647 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2013 ; 2.568 ; 2.646 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2518 ; 3.182 ; 3.956 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2519 ; 3.187 ; 3.957 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1884 ; 3.208 ; 2.924 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1884 ; 3.206 ; 2.923 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2723 ; 4.402 ; 4.229 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4652 ; 5.636 ;22.235 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4653 ; 5.637 ;22.242 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 4YMZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAR-15. REMARK 100 THE DEPOSITION ID IS D_1000207732. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.6 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM14 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95372 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54809 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 56.750 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : 11.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 4X22 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 8000, 1MM AMMONIUM SULFATE, REMARK 280 10MM EDTA, 1MM SODIUM AZIDE, 100MM BIS/TRIS, PH 6.6, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 75.67000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 37.83500 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.83500 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.67000 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: 3500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -21.0 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 A 405 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 410 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 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 ALA A 2 CB REMARK 470 LYS A 4 CE NZ REMARK 470 LYS A 18 CE NZ REMARK 470 ASP A 37 OD2 REMARK 470 LYS A 54 CD CE NZ REMARK 470 GLU A 57 OE1 REMARK 470 LYS A 86 CE NZ REMARK 470 LYS A 120 CD CE NZ REMARK 470 GLU A 122 CD OE1 OE2 REMARK 470 ILE A 149 CD1 REMARK 470 ARG A 150 CZ NH1 NH2 REMARK 470 LYS A 154 CD CE NZ REMARK 470 ASP A 157 CG OD1 OD2 REMARK 470 LEU A 166 CD1 REMARK 470 LYS A 194 CD CE NZ REMARK 470 ILE A 206 CD1 REMARK 470 ILE A 210 CD1 REMARK 470 LYS A 219 CE NZ REMARK 470 LYS A 228 NZ REMARK 470 LYS A 230 CE NZ REMARK 470 LYS A 243 CD CE NZ REMARK 470 ALA B 2 CB REMARK 470 LYS B 4 CD CE NZ REMARK 470 GLU B 29 CG CD OE1 OE2 REMARK 470 LYS B 30 CG CD CE NZ REMARK 470 LYS B 36 CG CD CE NZ REMARK 470 ASP B 37 OD2 REMARK 470 LYS B 54 CD CE NZ REMARK 470 GLU B 57 OE1 REMARK 470 LYS B 86 CE NZ REMARK 470 LYS B 91 CD CE NZ REMARK 470 LYS B 120 NZ REMARK 470 GLU B 122 OE2 REMARK 470 LYS B 154 CD CE NZ REMARK 470 LYS B 178 CE NZ REMARK 470 LYS B 194 CD CE NZ REMARK 470 LYS B 219 CE NZ REMARK 470 LEU B 227 CD1 CD2 REMARK 470 LYS B 228 CD CE NZ REMARK 470 LYS B 230 NZ REMARK 470 LYS B 243 CD CE NZ 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 O3 SO4 A 302 O HOH A 548 2.07 REMARK 500 O HOH A 556 O HOH A 558 2.10 REMARK 500 O HOH A 557 O HOH A 558 2.18 REMARK 500 O1 SO4 B 302 O HOH B 534 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 SER A 147 CB SER A 147 OG -0.102 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 136 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 193 NE - CZ - NH1 ANGL. DEV. = 3.4 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 -135.16 37.31 REMARK 500 LYS A 36 -115.30 60.96 REMARK 500 ALA A 74 -179.67 -179.78 REMARK 500 LYS B 12 -139.46 44.66 REMARK 500 LYS B 36 -119.72 67.72 REMARK 500 ALA B 74 -178.72 -172.90 REMARK 500 VAL B 201 102.64 64.70 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 13P A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 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 EDO A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 311 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 13P B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 308 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X22 RELATED DB: PDB REMARK 900 APO FORM STRUCTURE OF THE SAME ENZYME REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE REFERENCE SEQUENCE DATABASE DERIVED FROM STR. RGA DOES NOT REMARK 999 CURRENTLY EXIST. DBREF 4YMZ A 1 251 PDB 4YMZ 4YMZ 1 251 DBREF 4YMZ B 1 251 PDB 4YMZ 4YMZ 1 251 SEQRES 1 A 251 MET ALA ARG LYS THR ILE ILE ALA GLY ASN TRP LYS MET SEQRES 2 A 251 ASN LEU SER LEU LYS GLU ALA VAL PHE LEU ALA HIS SER SEQRES 3 A 251 ILE ARG GLU LYS ILE PRO SER ILE SER LYS ASP LYS VAL SEQRES 4 A 251 SER MET VAL PHE PRO SER THR LEU HIS LEU GLU ASN VAL SEQRES 5 A 251 SER LYS ILE LEU GLU GLY SER SER VAL ILE VAL GLY ALA SEQRES 6 A 251 GLN ASN CYS TYR HIS SER GLY LEU ALA ALA PHE THR GLY SEQRES 7 A 251 GLU THR SER PRO ASP GLN LEU LYS GLU ILE GLY VAL LYS SEQRES 8 A 251 VAL VAL MET VAL GLY HIS SER GLU ARG ARG GLN PHE LEU SEQRES 9 A 251 GLY GLU SER ASN PHE PHE CYS ASN ASP LYS ILE ARG PHE SEQRES 10 A 251 LEU LEU LYS ASN GLU PHE THR VAL LEU TYR CYS VAL GLY SEQRES 11 A 251 GLU THR LEU SER GLU ARG GLU SER GLY LYS THR LEU GLU SEQRES 12 A 251 VAL LEU SER SER GLN ILE ARG GLU GLY LEU LYS GLY ILE SEQRES 13 A 251 ASP SER VAL PHE PHE SER ASN LEU ILE LEU ALA TYR GLU SEQRES 14 A 251 PRO VAL TRP ALA ILE GLY THR GLY LYS VAL ALA THR PRO SEQRES 15 A 251 SER GLN ALA GLN GLU VAL HIS SER PHE ILE ARG LYS GLU SEQRES 16 A 251 ILE SER GLY LEU PHE VAL GLY ALA SER SER ILE SER GLU SEQRES 17 A 251 SER ILE SER ILE LEU TYR GLY GLY SER VAL LYS PRO ASP SEQRES 18 A 251 ASN ILE GLN ASP LEU LEU LYS GLU LYS ASP ILE ASP GLY SEQRES 19 A 251 GLY LEU VAL GLY GLY ALA SER GLN LYS ILE SER SER PHE SEQRES 20 A 251 ALA GLY LEU PHE SEQRES 1 B 251 MET ALA ARG LYS THR ILE ILE ALA GLY ASN TRP LYS MET SEQRES 2 B 251 ASN LEU SER LEU LYS GLU ALA VAL PHE LEU ALA HIS SER SEQRES 3 B 251 ILE ARG GLU LYS ILE PRO SER ILE SER LYS ASP LYS VAL SEQRES 4 B 251 SER MET VAL PHE PRO SER THR LEU HIS LEU GLU ASN VAL SEQRES 5 B 251 SER LYS ILE LEU GLU GLY SER SER VAL ILE VAL GLY ALA SEQRES 6 B 251 GLN ASN CYS TYR HIS SER GLY LEU ALA ALA PHE THR GLY SEQRES 7 B 251 GLU THR SER PRO ASP GLN LEU LYS GLU ILE GLY VAL LYS SEQRES 8 B 251 VAL VAL MET VAL GLY HIS SER GLU ARG ARG GLN PHE LEU SEQRES 9 B 251 GLY GLU SER ASN PHE PHE CYS ASN ASP LYS ILE ARG PHE SEQRES 10 B 251 LEU LEU LYS ASN GLU PHE THR VAL LEU TYR CYS VAL GLY SEQRES 11 B 251 GLU THR LEU SER GLU ARG GLU SER GLY LYS THR LEU GLU SEQRES 12 B 251 VAL LEU SER SER GLN ILE ARG GLU GLY LEU LYS GLY ILE SEQRES 13 B 251 ASP SER VAL PHE PHE SER ASN LEU ILE LEU ALA TYR GLU SEQRES 14 B 251 PRO VAL TRP ALA ILE GLY THR GLY LYS VAL ALA THR PRO SEQRES 15 B 251 SER GLN ALA GLN GLU VAL HIS SER PHE ILE ARG LYS GLU SEQRES 16 B 251 ILE SER GLY LEU PHE VAL GLY ALA SER SER ILE SER GLU SEQRES 17 B 251 SER ILE SER ILE LEU TYR GLY GLY SER VAL LYS PRO ASP SEQRES 18 B 251 ASN ILE GLN ASP LEU LEU LYS GLU LYS ASP ILE ASP GLY SEQRES 19 B 251 GLY LEU VAL GLY GLY ALA SER GLN LYS ILE SER SER PHE SEQRES 20 B 251 ALA GLY LEU PHE HET 13P A 301 10 HET SO4 A 302 5 HET EDO A 303 4 HET EDO A 304 4 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HET EDO A 309 4 HET EDO A 310 4 HET EDO A 311 4 HET 13P B 301 10 HET SO4 B 302 5 HET EDO B 303 4 HET EDO B 304 4 HET EDO B 305 4 HET EDO B 306 4 HET EDO B 307 4 HET EDO B 308 4 HETNAM 13P 1,3-DIHYDROXYACETONEPHOSPHATE HETNAM SO4 SULFATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 13P 2(C3 H7 O6 P) FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 EDO 15(C2 H6 O2) FORMUL 22 HOH *306(H2 O) HELIX 1 AA1 SER A 16 SER A 35 1 20 HELIX 2 AA2 SER A 45 LEU A 47 5 3 HELIX 3 AA3 HIS A 48 GLU A 57 1 10 HELIX 4 AA4 SER A 81 ILE A 88 1 8 HELIX 5 AA5 HIS A 97 LEU A 104 1 8 HELIX 6 AA6 SER A 107 ASN A 121 1 15 HELIX 7 AA7 THR A 132 SER A 138 1 7 HELIX 8 AA8 LYS A 140 LEU A 153 1 14 HELIX 9 AA9 ASP A 157 SER A 162 5 6 HELIX 10 AB1 PRO A 170 ILE A 174 5 5 HELIX 11 AB2 THR A 181 GLY A 198 1 18 HELIX 12 AB3 ALA A 203 GLU A 208 1 6 HELIX 13 AB4 LYS A 219 LYS A 228 1 10 HELIX 14 AB5 GLY A 238 GLN A 242 5 5 HELIX 15 AB6 LYS A 243 GLY A 249 1 7 HELIX 16 AB7 SER B 16 SER B 35 1 20 HELIX 17 AB8 SER B 45 LEU B 47 5 3 HELIX 18 AB9 HIS B 48 GLU B 57 1 10 HELIX 19 AC1 SER B 81 ILE B 88 1 8 HELIX 20 AC2 HIS B 97 LEU B 104 1 8 HELIX 21 AC3 SER B 107 ASN B 121 1 15 HELIX 22 AC4 THR B 132 SER B 138 1 7 HELIX 23 AC5 LYS B 140 LEU B 153 1 14 HELIX 24 AC6 ASP B 157 SER B 162 5 6 HELIX 25 AC7 PRO B 170 ILE B 174 5 5 HELIX 26 AC8 THR B 181 PHE B 200 1 20 HELIX 27 AC9 ALA B 203 ILE B 210 1 8 HELIX 28 AD1 ASN B 222 LYS B 228 1 7 HELIX 29 AD2 GLY B 238 GLN B 242 5 5 HELIX 30 AD3 LYS B 243 GLY B 249 1 7 SHEET 1 AA1 9 ILE A 6 ASN A 10 0 SHEET 2 AA1 9 VAL A 39 PHE A 43 1 O MET A 41 N GLY A 9 SHEET 3 AA1 9 VAL A 61 ALA A 65 1 O GLY A 64 N VAL A 42 SHEET 4 AA1 9 VAL A 92 VAL A 95 1 O MET A 94 N ALA A 65 SHEET 5 AA1 9 THR A 124 VAL A 129 1 O LEU A 126 N VAL A 95 SHEET 6 AA1 9 LEU A 164 TYR A 168 1 O ILE A 165 N TYR A 127 SHEET 7 AA1 9 ILE A 212 GLY A 215 1 O GLY A 215 N TYR A 168 SHEET 8 AA1 9 GLY A 234 VAL A 237 1 O GLY A 234 N TYR A 214 SHEET 9 AA1 9 ILE A 6 ASN A 10 1 N ALA A 8 O VAL A 237 SHEET 1 AA2 9 ILE B 6 ASN B 10 0 SHEET 2 AA2 9 VAL B 39 PHE B 43 1 O VAL B 39 N ILE B 7 SHEET 3 AA2 9 ILE B 62 ALA B 65 1 O GLY B 64 N VAL B 42 SHEET 4 AA2 9 VAL B 92 VAL B 95 1 O MET B 94 N ALA B 65 SHEET 5 AA2 9 THR B 124 VAL B 129 1 O LEU B 126 N VAL B 95 SHEET 6 AA2 9 LEU B 164 TYR B 168 1 O ALA B 167 N VAL B 129 SHEET 7 AA2 9 ILE B 212 GLY B 215 1 O LEU B 213 N LEU B 166 SHEET 8 AA2 9 GLY B 234 VAL B 237 1 O GLY B 234 N TYR B 214 SHEET 9 AA2 9 ILE B 6 ASN B 10 1 N ALA B 8 O GLY B 235 SITE 1 AC1 18 ASN A 10 LYS A 12 HIS A 97 GLU A 169 SITE 2 AC1 18 ALA A 173 ILE A 174 GLY A 175 SER A 217 SITE 3 AC1 18 LEU A 236 GLY A 238 GLY A 239 SO4 A 302 SITE 4 AC1 18 HOH A 451 HOH A 456 HOH A 537 HOH A 548 SITE 5 AC1 18 HOH A 551 HOH A 552 SITE 1 AC2 13 LYS A 12 ALA A 173 ILE A 174 GLY A 175 SITE 2 AC2 13 GLY A 216 SER A 217 GLY A 238 GLY A 239 SITE 3 AC2 13 13P A 301 HOH A 451 HOH A 456 HOH A 537 SITE 4 AC2 13 HOH A 548 SITE 1 AC3 4 GLU A 50 ASN A 51 GLU B 50 ASN B 51 SITE 1 AC4 3 ARG A 116 ILE A 156 PHE A 160 SITE 1 AC5 5 SER A 204 GLU A 208 HOH A 401 ARG B 136 SITE 2 AC5 5 GLN B 184 SITE 1 AC6 5 SER A 146 SER A 147 ARG A 150 GLU A 151 SITE 2 AC6 5 HOH A 463 SITE 1 AC7 5 LYS A 4 SER A 162 LEU A 164 ILE A 210 SITE 2 AC7 5 SER A 211 SITE 1 AC8 6 PRO A 220 ASP A 221 ASN A 222 ILE A 223 SITE 2 AC8 6 GLN A 224 ASP A 225 SITE 1 AC9 3 LEU A 104 HOH A 553 GLY B 105 SITE 1 AD1 3 GLU A 143 PHE A 191 HOH A 419 SITE 1 AD2 3 LEU B 133 TRP B 172 GLN B 184 SITE 1 AD3 17 ASN B 10 LYS B 12 HIS B 97 GLU B 169 SITE 2 AD3 17 ALA B 173 ILE B 174 GLY B 175 SER B 217 SITE 3 AD3 17 LEU B 236 GLY B 238 GLY B 239 SO4 B 302 SITE 4 AD3 17 HOH B 444 HOH B 501 HOH B 532 HOH B 533 SITE 5 AD3 17 HOH B 534 SITE 1 AD4 12 ALA B 173 ILE B 174 GLY B 175 SER B 217 SITE 2 AD4 12 GLY B 238 GLY B 239 13P B 301 HOH B 444 SITE 3 AD4 12 HOH B 501 HOH B 532 HOH B 533 HOH B 534 SITE 1 AD5 5 ARG B 116 LYS B 120 PHE B 160 HOH B 450 SITE 2 AD5 5 HOH B 524 SITE 1 AD6 5 ARG A 136 GLN A 184 GLY B 202 EDO B 305 SITE 2 AD6 5 HOH B 405 SITE 1 AD7 5 TRP A 172 LYS A 178 GLN A 184 EDO B 304 SITE 2 AD7 5 HOH B 404 SITE 1 AD8 1 VAL B 159 SITE 1 AD9 3 HIS B 70 PHE B 117 HOH B 539 SITE 1 AE1 3 HOH A 431 HOH A 553 PHE B 103 CRYST1 103.758 103.758 113.505 90.00 90.00 120.00 P 32 2 1 12 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 0.009638 0.005564 0.000000 0.00000 SCALE2 0.000000 0.011129 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008810 0.00000