HEADER TRANSFERASE 15-MAR-17 5XB5 TITLE CRYSTAL STRUCTURE OF R90A MUTANT OF THYMIDYLATE KINASE (AQ_969) FROM TITLE 2 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; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS (STRAIN VF5); SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: TMK, AQ_969; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KINASE, COMPLEX, NUCLEOTIDE BINDING, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.BISWAS,J.JEYAKANTHAN,K.SEKAR REVDAT 4 22-NOV-23 5XB5 1 REMARK REVDAT 3 30-AUG-17 5XB5 1 JRNL REVDAT 2 16-AUG-17 5XB5 1 JRNL REVDAT 1 28-JUN-17 5XB5 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 1742-4658 JRNL PMID 28627020 JRNL DOI 10.1111/FEBS.14140 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0155 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 18753 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) : 0.243 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 991 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) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.29 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1319 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.77 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 38 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -6.60000 REMARK 3 B22 (A**2) : 4.73000 REMARK 3 B33 (A**2) : -2.70000 REMARK 3 B12 (A**2) : 2.88000 REMARK 3 B13 (A**2) : -0.20000 REMARK 3 B23 (A**2) : 2.66000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.373 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.265 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.303 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.129 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.873 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3019 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2989 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4066 ; 1.855 ; 2.006 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6873 ; 1.136 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 7.354 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 124 ;41.171 ;25.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 568 ;17.441 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;20.844 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 483 ; 0.106 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3316 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 611 ; 0.003 ; 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): 1533 ; 0.558 ; 0.789 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1532 ; 0.556 ; 0.787 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1911 ; 1.024 ; 1.178 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1912 ; 1.024 ; 1.180 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1486 ; 0.546 ; 0.813 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1487 ; 0.545 ; 0.815 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2156 ; 0.890 ; 1.219 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3308 ; 4.902 ; 9.107 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3308 ; 4.902 ; 9.109 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 : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 195 1 REMARK 3 1 B 1 B 195 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 2879 ; 3.16 ; 0.50 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 1 A 193 REMARK 3 ORIGIN FOR THE GROUP (A): 16.3479 19.1952 22.5622 REMARK 3 T TENSOR REMARK 3 T11: 0.6088 T22: 0.0322 REMARK 3 T33: 0.4387 T12: -0.0061 REMARK 3 T13: 0.0920 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 3.3849 L22: 0.9166 REMARK 3 L33: 0.3241 L12: -0.2189 REMARK 3 L13: -0.3912 L23: -0.4593 REMARK 3 S TENSOR REMARK 3 S11: -0.2179 S12: -0.2175 S13: -0.6017 REMARK 3 S21: 0.0384 S22: 0.0786 S23: -0.0682 REMARK 3 S31: -0.0887 S32: -0.0107 S33: 0.1393 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 1 B 192 REMARK 3 ORIGIN FOR THE GROUP (A): 24.2540 45.6152 0.6232 REMARK 3 T TENSOR REMARK 3 T11: 0.7778 T22: 0.6024 REMARK 3 T33: 0.7428 T12: -0.3449 REMARK 3 T13: -0.0655 T23: 0.5233 REMARK 3 L TENSOR REMARK 3 L11: 3.5904 L22: 1.7201 REMARK 3 L33: 2.0793 L12: 0.5755 REMARK 3 L13: -0.6505 L23: -1.8558 REMARK 3 S TENSOR REMARK 3 S11: -0.7219 S12: 1.4267 S13: 1.1919 REMARK 3 S21: 0.1193 S22: 0.3154 S23: -0.2144 REMARK 3 S31: 0.0847 S32: -0.2717 S33: 0.4066 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 5XB5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1300003212. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : BRUKER AXS MICROSTAR REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRROR 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19751 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 53.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 68.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.55400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2PBR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 10% W/V POLYETHYLENE REMARK 280 GLYCOL 8000, 8% V/V ETHYLENE GLYCOL, PH 7.5, MICROBATCH, REMARK 280 TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -36.0 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 GLY A 191 REMARK 465 ARG A 194 REMARK 465 VAL A 195 REMARK 465 LEU B 193 REMARK 465 ARG B 194 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 LYS A 18 CD CE NZ REMARK 470 LYS A 27 NZ REMARK 470 GLU A 54 CG CD OE1 OE2 REMARK 470 ARG A 82 NE CZ NH1 NH2 REMARK 470 ARG A 138 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LYS A 143 CG CD CE NZ REMARK 470 ARG A 145 NE CZ NH1 NH2 REMARK 470 LYS A 164 CE NZ REMARK 470 GLU A 177 CD OE1 OE2 REMARK 470 GLU A 180 CG CD OE1 OE2 REMARK 470 LYS A 183 CG CD CE NZ REMARK 470 LEU A 193 CG CD1 CD2 REMARK 470 LYS B 18 NZ REMARK 470 LYS B 25 NZ REMARK 470 GLN B 26 CG CD OE1 NE2 REMARK 470 LYS B 41 CE NZ REMARK 470 GLU B 48 OE1 OE2 REMARK 470 GLU B 54 CG CD OE1 OE2 REMARK 470 LYS B 111 NZ REMARK 470 VAL B 133 CG1 CG2 REMARK 470 ASP B 134 CG OD1 OD2 REMARK 470 ARG B 138 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 139 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 141 CD CE NZ REMARK 470 LYS B 143 CG CD CE NZ REMARK 470 ARG B 145 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 157 CD CE NZ REMARK 470 GLU B 165 CG CD OE1 OE2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 GLU B 177 CG CD OE1 OE2 REMARK 470 GLU B 180 CD OE1 OE2 REMARK 470 VAL B 181 CG1 CG2 REMARK 470 GLU B 184 CG CD OE1 OE2 REMARK 470 ARG B 187 CG CD NE CZ NH1 NH2 REMARK 470 SER B 190 OG 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 94 CB SER A 94 OG -0.086 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 9 CB - CG - OD1 ANGL. DEV. = -7.9 DEGREES REMARK 500 ARG A 68 NE - CZ - NH1 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 ALA A 90 142.57 101.99 REMARK 500 PHE A 91 -145.28 -157.63 REMARK 500 ALA B 90 142.96 95.46 REMARK 500 PHE B 91 -150.40 -162.62 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 PO4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XAI RELATED DB: PDB REMARK 900 RELATED ID: 5XB2 RELATED DB: PDB REMARK 900 RELATED ID: 5XB3 RELATED DB: PDB REMARK 900 RELATED ID: 5XBH RELATED DB: PDB DBREF 5XB5 A 1 195 UNP O67099 KTHY_AQUAE 1 195 DBREF 5XB5 B 1 195 UNP O67099 KTHY_AQUAE 1 195 SEQADV 5XB5 ALA A 90 UNP O67099 ARG 90 ENGINEERED MUTATION SEQADV 5XB5 ALA B 90 UNP O67099 ARG 90 ENGINEERED MUTATION 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 ALA 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 ALA 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 PO4 A 201 5 HET PO4 B 201 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 2(O4 P 3-) FORMUL 5 HOH *38(H2 O) HELIX 1 AA1 GLY A 12 LYS A 27 1 16 HELIX 2 AA2 THR A 40 GLU A 53 1 14 HELIX 3 AA3 ASP A 56 LYS A 75 1 20 HELIX 4 AA4 LYS A 75 ARG A 82 1 8 HELIX 5 AA5 PHE A 91 GLY A 100 1 10 HELIX 6 AA6 ASP A 106 THR A 118 1 13 HELIX 7 AA7 PRO A 132 GLU A 142 1 11 HELIX 8 AA8 ASN A 148 GLU A 166 1 19 HELIX 9 AA9 GLU A 177 SER A 190 1 14 HELIX 10 AB1 GLY B 12 LYS B 27 1 16 HELIX 11 AB2 THR B 40 GLU B 53 1 14 HELIX 12 AB3 ASP B 56 LYS B 75 1 20 HELIX 13 AB4 LYS B 75 ARG B 82 1 8 HELIX 14 AB5 PHE B 91 GLY B 100 1 10 HELIX 15 AB6 ASP B 106 ARG B 119 1 14 HELIX 16 AB7 PRO B 132 LYS B 143 1 12 HELIX 17 AB8 ASN B 148 GLU B 166 1 19 HELIX 18 AB9 GLU B 177 SER B 190 1 14 SHEET 1 AA1 5 VAL A 31 ARG A 35 0 SHEET 2 AA1 5 VAL A 85 ASP A 89 1 O ASP A 89 N TYR A 34 SHEET 3 AA1 5 LEU A 2 GLU A 6 1 N ILE A 3 O VAL A 86 SHEET 4 AA1 5 ILE A 125 ASP A 130 1 O LEU A 127 N ALA A 4 SHEET 5 AA1 5 VAL A 169 ASP A 173 1 O ILE A 172 N LEU A 128 SHEET 1 AA2 5 VAL B 31 ARG B 35 0 SHEET 2 AA2 5 VAL B 85 ASP B 89 1 O ASP B 89 N TYR B 34 SHEET 3 AA2 5 LEU B 2 GLU B 6 1 N PHE B 5 O LEU B 88 SHEET 4 AA2 5 ILE B 125 ASP B 130 1 O LEU B 127 N ALA B 4 SHEET 5 AA2 5 VAL B 169 ASP B 173 1 O ILE B 172 N LEU B 128 CISPEP 1 GLU A 36 PRO A 37 0 -1.16 CISPEP 2 GLU B 36 PRO B 37 0 -1.21 SITE 1 AC1 5 GLY A 10 SER A 11 GLY A 12 LYS A 13 SITE 2 AC1 5 THR A 14 SITE 1 AC2 5 GLY B 10 SER B 11 GLY B 12 LYS B 13 SITE 2 AC2 5 THR B 14 CRYST1 43.010 51.840 53.640 92.17 92.67 112.83 P 1 2 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 0.023250 0.009788 0.001682 0.00000 SCALE2 0.000000 0.020930 0.001274 0.00000 SCALE3 0.000000 0.000000 0.018698 0.00000 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 MTRIX1 2 -0.999992 -0.003523 -0.002080 40.56262 1 MTRIX2 2 -0.001378 -0.188573 0.982058 27.40212 1 MTRIX3 2 -0.003852 0.982053 0.188567 -22.39915 1