PDB Short entry for 4S35 HEADER TRANSFERASE 26-JAN-15 4S35 TITLE AMPPCP AND TMP BOUND CRYSTAL STRUCTURE OF THYMIDYLATE KINASE (AQ_969) TITLE 2 FROM AQUIFEX AEOLICUS VF5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMIDYLATE KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DTMP KINASE; COMPND 5 EC: 2.7.4.9; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: AQ_969, TMK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS (DE3)-RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS TRANSFERASE, ATP BINDING, TMP BINDING EXPDTA X-RAY DIFFRACTION AUTHOR A.BISWAS,J.JEYAKANTHAN,K.SEKAR,S.KURAMITSU,S.YOKOYAMA REVDAT 4 20-SEP-23 4S35 1 REMARK REVDAT 3 24-AUG-22 4S35 1 JRNL REMARK LINK REVDAT 2 28-JUN-17 4S35 1 JRNL REVDAT 1 27-JAN-16 4S35 0 JRNL AUTH A.BISWAS,A.SHUKLA,S.K.CHAUDHARY,R.SANTHOSH,J.JEYAKANTHAN, JRNL AUTH 2 K.SEKAR JRNL TITL STRUCTURAL STUDIES OF A HYPERTHERMOPHILIC THYMIDYLATE KINASE JRNL TITL 2 ENZYME REVEAL CONFORMATIONAL SUBSTATES ALONG THE REACTION JRNL TITL 3 COORDINATE. JRNL REF FEBS J. V. 284 2527 2017 JRNL REFN ISSN 1742-464X JRNL PMID 28627020 JRNL DOI 10.1111/FEBS.14140 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 51970 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) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.174 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2809 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3389 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.1790 REMARK 3 BIN FREE R VALUE SET COUNT : 207 REMARK 3 BIN FREE R VALUE : 0.2090 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3071 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 117 REMARK 3 SOLVENT ATOMS : 354 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.77000 REMARK 3 B22 (A**2) : 1.39000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.073 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.200 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3345 ; 0.024 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3326 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4542 ; 2.473 ; 2.050 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7673 ; 1.026 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 417 ; 6.107 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 140 ;37.423 ;24.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 641 ;12.157 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;17.223 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 530 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3604 ; 0.012 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 689 ; 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): 1588 ; 1.675 ; 1.278 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1587 ; 1.674 ; 1.277 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1989 ; 2.454 ; 1.917 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1990 ; 2.454 ; 1.919 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1757 ; 2.568 ; 1.501 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1757 ; 2.563 ; 1.501 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2539 ; 3.848 ; 2.149 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4096 ; 5.468 ;11.458 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3911 ; 5.265 ;10.820 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 4S35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-JAN-15. REMARK 100 THE DEPOSITION ID IS D_1000088120. 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 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : RH COATED BENT-CYRINDRICAL REMARK 200 MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 54781 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.15800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.376 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: PDB ENTRY 2PBR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 NAACETATE PH 5.4, 0.2 M REMARK 280 MGFORMATE,10 MM DTMP, 10MM AMP-PCP, 10 MM MGCL2, 20% GLYCEROL AS REMARK 280 CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 31.30750 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: 5690 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16270 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -76.0 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 VAL B 195 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 GLU A 48 CD OE1 OE2 REMARK 470 GLU A 54 CG CD OE1 OE2 REMARK 470 GLU A 115 OE1 OE2 REMARK 470 LYS A 122 CE NZ REMARK 470 ARG A 138 CD NE CZ NH1 NH2 REMARK 470 LYS A 141 CD CE NZ REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 157 CE NZ REMARK 470 LYS A 164 CE NZ REMARK 470 GLU A 167 CD OE1 OE2 REMARK 470 GLU A 177 CD OE1 OE2 REMARK 470 LYS B 18 NZ REMARK 470 LYS B 25 NZ REMARK 470 LYS B 27 NZ REMARK 470 GLU B 48 CD OE1 OE2 REMARK 470 GLU B 54 CG CD OE1 OE2 REMARK 470 ARG B 82 NE CZ NH1 NH2 REMARK 470 LYS B 141 CG CD CE NZ REMARK 470 GLU B 142 CG CD OE1 OE2 REMARK 470 LYS B 149 CE NZ REMARK 470 LYS B 157 CE NZ REMARK 470 GLU B 165 CG CD OE1 OE2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 ARG B 187 CD NE CZ NH1 NH2 REMARK 470 ARG B 194 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 382 O HOH A 383 1.89 REMARK 500 O HOH B 331 O HOH B 332 1.94 REMARK 500 O3P TMP A 202 O HOH A 457 2.06 REMARK 500 O HOH A 433 O HOH A 446 2.09 REMARK 500 NZ LYS A 18 O HOH A 416 2.13 REMARK 500 O HOH B 424 O HOH B 425 2.14 REMARK 500 OE1 GLU B 57 O HOH B 406 2.19 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 6 CG GLU A 6 CD 0.108 REMARK 500 GLU A 6 CD GLU A 6 OE2 -0.133 REMARK 500 GLU B 6 CD GLU B 6 OE2 -0.069 REMARK 500 TYR B 29 CB TYR B 29 CG -0.093 REMARK 500 GLU B 65 CD GLU B 65 OE2 0.075 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 56 CB - CG - OD2 ANGL. DEV. = -6.6 DEGREES REMARK 500 ARG A 58 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 58 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 ASP A 79 CB - CG - OD1 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 106 CB - CG - OD2 ANGL. DEV. = 7.0 DEGREES REMARK 500 GLU B 6 OE1 - CD - OE2 ANGL. DEV. = 14.4 DEGREES REMARK 500 ASP B 56 CB - CG - OD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ASP B 79 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP B 106 CB - CG - OD1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ASP B 124 CB - CG - OD1 ANGL. DEV. = 6.9 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 75 -57.44 -123.66 REMARK 500 ARG A 90 147.48 78.63 REMARK 500 PHE A 91 -140.61 -155.25 REMARK 500 LYS B 27 1.66 -67.92 REMARK 500 ARG B 90 147.05 79.02 REMARK 500 PHE B 91 -144.48 -155.20 REMARK 500 LYS B 141 -102.16 -93.83 REMARK 500 GLU B 147 67.05 -102.91 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 MG A 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 14 OG1 REMARK 620 2 ACP A 201 O2G 175.1 REMARK 620 3 ACP A 201 O1B 87.9 95.3 REMARK 620 4 HOH A 301 O 89.2 94.6 88.6 REMARK 620 5 HOH A 302 O 87.9 88.2 92.6 176.8 REMARK 620 6 HOH A 303 O 92.6 84.5 175.5 87.0 91.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR B 14 OG1 REMARK 620 2 ACP B 201 O1G 175.5 REMARK 620 3 ACP B 201 O1B 89.2 93.4 REMARK 620 4 HOH B 301 O 87.8 88.5 92.1 REMARK 620 5 HOH B 302 O 89.2 94.6 87.9 177.0 REMARK 620 6 HOH B 303 O 89.8 87.9 174.2 93.6 86.3 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 ACP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TMP A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACP B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TMP B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO B 206 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2PBR RELATED DB: PDB REMARK 900 THE SAME PROTEIN FROM AQUIFEX AEOLICUS VF5 IN SULFATE BOUND FORM DBREF 4S35 A 1 195 UNP O67099 KTHY_AQUAE 1 195 DBREF 4S35 B 1 195 UNP O67099 KTHY_AQUAE 1 195 SEQRES 1 A 195 MET LEU ILE ALA PHE GLU GLY ILE ASP GLY SER GLY LYS SEQRES 2 A 195 THR THR GLN ALA LYS LYS LEU TYR GLU TYR LEU LYS GLN SEQRES 3 A 195 LYS GLY TYR PHE VAL SER LEU TYR ARG GLU PRO GLY GLY SEQRES 4 A 195 THR LYS VAL GLY GLU VAL LEU ARG GLU ILE LEU LEU THR SEQRES 5 A 195 GLU GLU LEU ASP GLU ARG THR GLU LEU LEU LEU PHE GLU SEQRES 6 A 195 ALA SER ARG SER LYS LEU ILE GLU GLU LYS ILE ILE PRO SEQRES 7 A 195 ASP LEU LYS ARG ASP LYS VAL VAL ILE LEU ASP ARG PHE SEQRES 8 A 195 VAL LEU SER THR ILE ALA TYR GLN GLY TYR GLY LYS GLY SEQRES 9 A 195 LEU ASP VAL GLU PHE ILE LYS ASN LEU ASN GLU PHE ALA SEQRES 10 A 195 THR ARG GLY VAL LYS PRO ASP ILE THR LEU LEU LEU ASP SEQRES 11 A 195 ILE PRO VAL ASP ILE ALA LEU ARG ARG LEU LYS GLU LYS SEQRES 12 A 195 ASN ARG PHE GLU ASN LYS GLU PHE LEU GLU LYS VAL ARG SEQRES 13 A 195 LYS GLY PHE LEU GLU LEU ALA LYS GLU GLU GLU ASN VAL SEQRES 14 A 195 VAL VAL ILE ASP ALA SER GLY GLU GLU GLU GLU VAL PHE SEQRES 15 A 195 LYS GLU ILE LEU ARG ALA LEU SER GLY VAL LEU ARG VAL SEQRES 1 B 195 MET LEU ILE ALA PHE GLU GLY ILE ASP GLY SER GLY LYS SEQRES 2 B 195 THR THR GLN ALA LYS LYS LEU TYR GLU TYR LEU LYS GLN SEQRES 3 B 195 LYS GLY TYR PHE VAL SER LEU TYR ARG GLU PRO GLY GLY SEQRES 4 B 195 THR LYS VAL GLY GLU VAL LEU ARG GLU ILE LEU LEU THR SEQRES 5 B 195 GLU GLU LEU ASP GLU ARG THR GLU LEU LEU LEU PHE GLU SEQRES 6 B 195 ALA SER ARG SER LYS LEU ILE GLU GLU LYS ILE ILE PRO SEQRES 7 B 195 ASP LEU LYS ARG ASP LYS VAL VAL ILE LEU ASP ARG PHE SEQRES 8 B 195 VAL LEU SER THR ILE ALA TYR GLN GLY TYR GLY LYS GLY SEQRES 9 B 195 LEU ASP VAL GLU PHE ILE LYS ASN LEU ASN GLU PHE ALA SEQRES 10 B 195 THR ARG GLY VAL LYS PRO ASP ILE THR LEU LEU LEU ASP SEQRES 11 B 195 ILE PRO VAL ASP ILE ALA LEU ARG ARG LEU LYS GLU LYS SEQRES 12 B 195 ASN ARG PHE GLU ASN LYS GLU PHE LEU GLU LYS VAL ARG SEQRES 13 B 195 LYS GLY PHE LEU GLU LEU ALA LYS GLU GLU GLU ASN VAL SEQRES 14 B 195 VAL VAL ILE ASP ALA SER GLY GLU GLU GLU GLU VAL PHE SEQRES 15 B 195 LYS GLU ILE LEU ARG ALA LEU SER GLY VAL LEU ARG VAL HET ACP A 201 31 HET TMP A 202 42 HET MG A 203 1 HET MG A 204 1 HET EDO A 205 4 HET ACP B 201 31 HET TMP B 202 21 HET MG B 203 1 HET MG B 204 1 HET CL B 205 1 HET EDO B 206 4 HETNAM ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER HETNAM TMP THYMIDINE-5'-PHOSPHATE HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETNAM CL CHLORIDE ION HETSYN ACP ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ACP 2(C11 H18 N5 O12 P3) FORMUL 4 TMP 2(C10 H15 N2 O8 P) FORMUL 5 MG 4(MG 2+) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 12 CL CL 1- FORMUL 14 HOH *354(H2 O) HELIX 1 1 GLY A 12 LYS A 27 1 16 HELIX 2 2 THR A 40 GLU A 53 1 14 HELIX 3 3 ASP A 56 LYS A 75 1 20 HELIX 4 4 LYS A 75 ARG A 82 1 8 HELIX 5 5 PHE A 91 GLY A 100 1 10 HELIX 6 6 ASP A 106 ARG A 119 1 14 HELIX 7 7 PRO A 132 ARG A 139 1 8 HELIX 8 8 ASN A 148 GLU A 166 1 19 HELIX 9 9 GLU A 177 SER A 190 1 14 HELIX 10 10 GLY B 12 LYS B 27 1 16 HELIX 11 11 THR B 40 GLU B 53 1 14 HELIX 12 12 ASP B 56 LYS B 75 1 20 HELIX 13 13 LYS B 75 ARG B 82 1 8 HELIX 14 14 PHE B 91 GLY B 100 1 10 HELIX 15 15 ASP B 106 ARG B 119 1 14 HELIX 16 16 PRO B 132 LEU B 140 1 9 HELIX 17 17 ASN B 148 GLU B 166 1 19 HELIX 18 18 GLU B 177 SER B 190 1 14 SHEET 1 A 5 VAL A 31 ARG A 35 0 SHEET 2 A 5 VAL A 85 ASP A 89 1 O ASP A 89 N TYR A 34 SHEET 3 A 5 LEU A 2 GLU A 6 1 N ILE A 3 O VAL A 86 SHEET 4 A 5 ILE A 125 ASP A 130 1 O LEU A 127 N ALA A 4 SHEET 5 A 5 VAL A 169 ASP A 173 1 O ILE A 172 N LEU A 128 SHEET 1 B 5 VAL B 31 ARG B 35 0 SHEET 2 B 5 VAL B 85 ASP B 89 1 O ASP B 89 N TYR B 34 SHEET 3 B 5 LEU B 2 GLU B 6 1 N PHE B 5 O LEU B 88 SHEET 4 B 5 ILE B 125 ASP B 130 1 O LEU B 127 N ALA B 4 SHEET 5 B 5 VAL B 169 ASP B 173 1 O ILE B 172 N LEU B 128 LINK OG1 THR A 14 MG MG A 203 1555 1555 2.08 LINK O ASP A 83 MG MG A 204 1555 1555 2.89 LINK O2G ACP A 201 MG MG A 203 1555 1555 2.03 LINK O1B ACP A 201 MG MG A 203 1555 1555 2.09 LINK MG MG A 203 O HOH A 301 1555 1555 2.07 LINK MG MG A 203 O HOH A 302 1555 1555 2.08 LINK MG MG A 203 O HOH A 303 1555 1555 2.13 LINK OG1 THR B 14 MG MG B 203 1555 1555 2.11 LINK OE1 GLU B 153 MG MG B 204 1555 1555 2.53 LINK O1G ACP B 201 MG MG B 203 1555 1555 2.07 LINK O1B ACP B 201 MG MG B 203 1555 1555 2.15 LINK MG MG B 203 O HOH B 301 1555 1555 2.08 LINK MG MG B 203 O HOH B 302 1555 1555 2.09 LINK MG MG B 203 O HOH B 303 1555 1555 2.04 CISPEP 1 GLU A 36 PRO A 37 0 -11.76 CISPEP 2 GLU B 36 PRO B 37 0 -9.22 SITE 1 AC1 24 ASP A 9 GLY A 10 SER A 11 GLY A 12 SITE 2 AC1 24 LYS A 13 THR A 14 THR A 15 ARG A 90 SITE 3 AC1 24 ARG A 139 GLU A 147 GLY A 176 GLU A 178 SITE 4 AC1 24 TMP A 202 MG A 203 HOH A 301 HOH A 302 SITE 5 AC1 24 HOH A 303 HOH A 397 HOH A 398 HOH A 399 SITE 6 AC1 24 HOH A 404 HOH A 407 HOH A 408 HOH A 485 SITE 1 AC2 17 ASP A 9 GLU A 36 PRO A 37 ARG A 47 SITE 2 AC2 17 PHE A 64 ARG A 90 THR A 95 TYR A 98 SITE 3 AC2 17 GLN A 99 ASN A 144 PHE A 146 ACP A 201 SITE 4 AC2 17 HOH A 302 HOH A 303 HOH A 408 HOH A 409 SITE 5 AC2 17 HOH A 457 SITE 1 AC3 5 THR A 14 ACP A 201 HOH A 301 HOH A 302 SITE 2 AC3 5 HOH A 303 SITE 1 AC4 5 TYR A 29 PHE A 30 ASP A 83 ASN A 148 SITE 2 AC4 5 GLU A 150 SITE 1 AC5 4 ASP A 134 ILE A 135 ARG A 138 HOH A 359 SITE 1 AC6 24 ASP B 9 GLY B 10 SER B 11 GLY B 12 SITE 2 AC6 24 LYS B 13 THR B 14 THR B 15 ARG B 90 SITE 3 AC6 24 ARG B 139 GLU B 147 GLY B 176 GLU B 177 SITE 4 AC6 24 GLU B 178 TMP B 202 MG B 203 HOH B 301 SITE 5 AC6 24 HOH B 302 HOH B 303 HOH B 323 HOH B 369 SITE 6 AC6 24 HOH B 372 HOH B 374 HOH B 375 HOH B 376 SITE 1 AC7 16 ASP B 9 GLU B 36 PRO B 37 ARG B 47 SITE 2 AC7 16 PHE B 64 ARG B 90 THR B 95 TYR B 98 SITE 3 AC7 16 GLN B 99 ASN B 144 PHE B 146 ACP B 201 SITE 4 AC7 16 HOH B 301 HOH B 303 HOH B 323 HOH B 358 SITE 1 AC8 5 THR B 14 ACP B 201 HOH B 301 HOH B 302 SITE 2 AC8 5 HOH B 303 SITE 1 AC9 3 VAL B 133 GLU B 153 ARG B 156 SITE 1 BC1 1 ASN B 114 SITE 1 BC2 2 VAL A 195 GLU B 179 CRYST1 42.479 62.615 73.577 90.00 97.97 90.00 P 1 21 1 4 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 0.023541 0.000000 0.003294 0.00000 SCALE2 0.000000 0.015971 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013724 0.00000