HEADER HYDROLASE 13-MAR-20 6M69 TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1 IN COMPLEX WITH TITLE 2 GMPPCP (GDP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROLASE, NUDIX FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOLICIBACTERIUM SMEGMATIS MC2 155; SOURCE 3 ORGANISM_TAXID: 246196; SOURCE 4 STRAIN: MC2 155; SOURCE 5 GENE: MSMEG_2390; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JW0097 KEYWDS MSMUTT1, NUDIX HYDROLASE, HISTIDINE PHOSPHATASE DOMAIN, NUCLEOTIDE KEYWDS 2 POOL SANITATION ENZYME, GMPPCP, MOLECULAR AGGREGATION, PLASTICITY, KEYWDS 3 ENZYME ACTION, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.RAJ,S.KARTHIK,S.M.ARIF,U.VARSHNEY,M.VIJAYAN REVDAT 3 29-NOV-23 6M69 1 REMARK REVDAT 2 28-OCT-20 6M69 1 REMARK REVDAT 1 14-OCT-20 6M69 0 JRNL AUTH P.RAJ,S.KARTHIK,S.M.ARIF,U.VARSHNEY,M.VIJAYAN JRNL TITL PLASTICITY, LIGAND CONFORMATION AND ENZYME ACTION OF JRNL TITL 2 MYCOBACTERIUM SMEGMATIS MUTT1. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 982 2020 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 33021500 JRNL DOI 10.1107/S2059798320010992 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.M.ARIF,A.G.PATIL,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL BIOCHEMICAL AND STRUCTURAL STUDIES OF MYCOBACTERIUM REMARK 1 TITL 2 SMEGMATIS MUTT1, A SANITIZATION ENZYME WITH UNUSUAL MODES OF REMARK 1 TITL 3 ASSOCIATION. REMARK 1 REF ACTA CRYSTALLOGR D STRUCT V. 73 349 2017 REMARK 1 REF 2 BIOL REMARK 1 REFN ISSN 2059-7983 REMARK 1 PMID 28375146 REMARK 1 DOI 10.1107/S2059798317002534 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.M.ARIF,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL HYDROLYSIS OF DIADENOSINE POLYPHOSPHATES. EXPLORATION OF AN REMARK 1 TITL 2 ADDITIONAL ROLE OF MYCOBACTERIUM SMEGMATIS MUTT1. REMARK 1 REF J. STRUCT. BIOL. V. 199 165 2017 REMARK 1 REFN ESSN 1095-8657 REMARK 1 PMID 28705712 REMARK 1 DOI 10.1016/J.JSB.2017.07.002 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.82 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 49683 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2667 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3623 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE SET COUNT : 201 REMARK 3 BIN FREE R VALUE : 0.2770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2248 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 371 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.72000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.75000 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): 0.077 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.080 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.512 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2440 ; 0.017 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2268 ; 0.034 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3345 ; 1.983 ; 1.679 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5236 ; 2.367 ; 1.588 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 314 ; 6.274 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 139 ;25.815 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 391 ;12.726 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 28 ;17.639 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 313 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2772 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 544 ; 0.016 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 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 : 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: INDIVIDUAL ISOTROPIC B-FACTOR REMARK 3 REFINEMENT REMARK 4 REMARK 4 6M69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-20. REMARK 100 THE DEPOSITION ID IS D_1300016165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 52698 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 36.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.61000 REMARK 200 R SYM FOR SHELL (I) : 0.61000 REMARK 200 FOR SHELL : 1.200 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: 5GG5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE, 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE, 30% W/V PEG 4000, PH 4.6, MICROBATCH, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 96.32500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.54000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 96.32500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 18.54000 REMARK 290 SMTRY3 4 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET A 2 REMARK 465 PRO A 3 REMARK 465 VAL A 4 REMARK 465 ASP A 5 REMARK 465 ASP A 6 REMARK 465 LEU A 7 REMARK 465 GLN A 8 REMARK 465 GLU A 9 REMARK 465 ILE A 10 REMARK 465 PRO A 11 REMARK 465 LEU A 12 REMARK 465 SER A 13 REMARK 465 LYS A 14 REMARK 465 ASP A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 LYS A 19 REMARK 465 SER A 20 REMARK 465 LYS A 21 REMARK 465 SER A 36 REMARK 465 GLU A 37 REMARK 465 HIS A 38 REMARK 465 GLY A 39 REMARK 465 GLY A 40 REMARK 465 THR A 41 REMARK 465 THR A 42 REMARK 465 GLY A 43 REMARK 465 HIS A 44 REMARK 465 PRO A 45 REMARK 465 ALA A 46 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 HIS A 22 CG ND1 CD2 CE1 NE2 REMARK 470 ASP A 126 CG OD1 OD2 REMARK 470 LYS A 150 CG CD CE NZ REMARK 470 ARG A 175 CD NE CZ NH1 NH2 REMARK 470 ARG A 178 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 180 CG CD CE NZ REMARK 470 ARG A 184 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 254 CD CE NZ REMARK 470 ARG A 289 CD NE CZ NH1 NH2 REMARK 470 LYS A 322 CG CD CE NZ 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 81 CD GLU A 81 OE2 -0.072 REMARK 500 GLU A 84 CD GLU A 84 OE1 -0.084 REMARK 500 GLU A 242 CD GLU A 242 OE1 -0.087 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 158 CG - CD - NE ANGL. DEV. = 16.5 DEGREES REMARK 500 ARG A 193 CG - CD - NE ANGL. DEV. = -15.2 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 ASP A 59 66.92 61.22 REMARK 500 ALA A 173 27.08 -145.40 REMARK 500 ASP A 248 77.81 -150.81 REMARK 500 THR A 270 -154.86 -142.31 REMARK 500 ASN A 295 31.92 -156.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL A 99 10.18 REMARK 500 VAL A 99 10.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 869 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH A 870 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH A 871 DISTANCE = 6.04 ANGSTROMS 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 405 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 101 OH REMARK 620 2 GDP A 401 O1A 123.3 REMARK 620 3 GDP A 401 O2A 67.4 80.0 REMARK 620 4 GDP A 401 O5' 130.4 68.1 68.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue POP A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 405 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6M65 RELATED DB: PDB REMARK 900 6M65 CONTAINS THE SAME PROTEIN COMPLEXED WITH GMPPNP (GDP) DBREF 6M69 A 1 322 UNP A0QUZ2 A0QUZ2_MYCS2 1 322 SEQADV 6M69 MET A -19 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 GLY A -18 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 SER A -17 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 SER A -16 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 HIS A -15 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 HIS A -14 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 HIS A -13 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 HIS A -12 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 HIS A -11 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 HIS A -10 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 SER A -9 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 SER A -8 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 GLY A -7 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 LEU A -6 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 VAL A -5 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 PRO A -4 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 ARG A -3 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 GLY A -2 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 SER A -1 UNP A0QUZ2 EXPRESSION TAG SEQADV 6M69 HIS A 0 UNP A0QUZ2 EXPRESSION TAG SEQRES 1 A 342 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 342 LEU VAL PRO ARG GLY SER HIS MET MET PRO VAL ASP ASP SEQRES 3 A 342 LEU GLN GLU ILE PRO LEU SER LYS ASP THR THR GLU LYS SEQRES 4 A 342 SER LYS HIS THR VAL ARG ALA ALA GLY ALA VAL LEU TRP SEQRES 5 A 342 ARG ASP ALA SER GLU HIS GLY GLY THR THR GLY HIS PRO SEQRES 6 A 342 ALA THR VAL GLU VAL ALA VAL ILE HIS ARG PRO ARG TYR SEQRES 7 A 342 ASP ASP TRP SER LEU PRO LYS GLY LYS LEU ASP GLN GLY SEQRES 8 A 342 GLU THR GLU PRO VAL ALA ALA ALA ARG GLU ILE HIS GLU SEQRES 9 A 342 GLU THR GLY HIS THR ALA VAL LEU GLY ARG ARG LEU GLY SEQRES 10 A 342 ARG VAL THR TYR PRO ILE PRO GLN GLY THR LYS ARG VAL SEQRES 11 A 342 TRP TYR TRP ALA ALA LYS SER THR GLY GLY ASP PHE SER SEQRES 12 A 342 PRO ASN ASP GLU VAL ASP LYS LEU VAL TRP LEU PRO VAL SEQRES 13 A 342 ASP ALA ALA MET ASP GLN LEU GLN TYR PRO ASP ASP ARG SEQRES 14 A 342 LYS VAL LEU ARG ARG PHE VAL LYS ARG PRO VAL ASP THR SEQRES 15 A 342 LYS THR VAL LEU VAL VAL ARG HIS GLY THR ALA GLY ARG SEQRES 16 A 342 ARG SER ARG TYR LYS GLY ASP ASP ARG LYS ARG PRO LEU SEQRES 17 A 342 ASP LYS ARG GLY ARG ALA GLN ALA GLU ALA LEU VAL ALA SEQRES 18 A 342 GLN LEU MET ALA PHE GLY ALA THR THR LEU TYR ALA ALA SEQRES 19 A 342 ASP ARG VAL ARG CYS HIS GLN THR ILE GLU PRO LEU ALA SEQRES 20 A 342 GLN GLU LEU ASP GLN LEU ILE HIS ASN GLU PRO LEU LEU SEQRES 21 A 342 THR GLU GLU ALA TYR ALA ALA ASP HIS LYS ALA ALA ARG SEQRES 22 A 342 LYS ARG LEU LEU GLU ILE ALA GLY ARG PRO GLY ASN PRO SEQRES 23 A 342 VAL ILE CYS THR GLN GLY LYS VAL ILE PRO GLY LEU ILE SEQRES 24 A 342 GLU TRP TRP CYS GLU ARG ALA LYS VAL ARG PRO GLU THR SEQRES 25 A 342 THR GLY ASN ARG LYS GLY SER THR TRP VAL LEU SER LEU SEQRES 26 A 342 SER ASP GLY GLU LEU VAL GLY ALA ASP TYR LEU SER PRO SEQRES 27 A 342 PRO ASP GLU LYS HET GDP A 401 28 HET POP A 402 9 HET EDO A 403 4 HET EDO A 404 4 HET MG A 405 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM POP PYROPHOSPHATE 2- HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 POP H2 O7 P2 2- FORMUL 4 EDO 2(C2 H6 O2) FORMUL 6 MG MG 2+ FORMUL 7 HOH *371(H2 O) HELIX 1 AA1 THR A 73 GLY A 87 1 15 HELIX 2 AA2 PRO A 135 LEU A 143 1 9 HELIX 3 AA3 TYR A 145 LYS A 157 1 13 HELIX 4 AA4 ASP A 182 ARG A 186 5 5 HELIX 5 AA5 ASP A 189 PHE A 206 1 18 HELIX 6 AA6 ARG A 216 ASP A 231 1 16 HELIX 7 AA7 PRO A 238 LEU A 240 5 3 HELIX 8 AA8 THR A 241 ASP A 248 1 8 HELIX 9 AA9 ASP A 248 ARG A 262 1 15 HELIX 10 AB1 VAL A 274 LYS A 287 1 14 SHEET 1 AA1 5 ASP A 60 SER A 62 0 SHEET 2 AA1 5 GLU A 49 ARG A 55 -1 N ILE A 53 O SER A 62 SHEET 3 AA1 5 THR A 23 ARG A 33 -1 N LEU A 31 O ALA A 51 SHEET 4 AA1 5 GLY A 106 GLY A 120 1 O THR A 107 N VAL A 24 SHEET 5 AA1 5 HIS A 88 ILE A 103 -1 N LEU A 96 O TYR A 112 SHEET 1 AA2 4 LYS A 65 LYS A 67 0 SHEET 2 AA2 4 THR A 23 ARG A 33 -1 N ALA A 27 O GLY A 66 SHEET 3 AA2 4 GLU A 49 ARG A 55 -1 O ALA A 51 N LEU A 31 SHEET 4 AA2 4 LYS A 130 LEU A 134 -1 O LEU A 134 N VAL A 50 SHEET 1 AA3 6 ILE A 234 GLU A 237 0 SHEET 2 AA3 6 THR A 210 ALA A 214 1 N LEU A 211 O HIS A 235 SHEET 3 AA3 6 PRO A 266 THR A 270 1 O CYS A 269 N ALA A 214 SHEET 4 AA3 6 LYS A 163 ARG A 169 1 N LEU A 166 O PRO A 266 SHEET 5 AA3 6 THR A 300 SER A 306 -1 O LEU A 303 N VAL A 165 SHEET 6 AA3 6 GLU A 309 LEU A 316 -1 O LEU A 316 N THR A 300 LINK OH TYR A 101 MG MG A 405 1555 1555 2.78 LINK O1A GDP A 401 MG MG A 405 1555 1555 2.03 LINK O2A GDP A 401 MG MG A 405 1555 1555 1.84 LINK O5' GDP A 401 MG MG A 405 1555 1555 2.39 SITE 1 AC1 17 ARG A 55 TYR A 58 LYS A 65 TYR A 101 SITE 2 AC1 17 LYS A 108 TYR A 145 MG A 405 HOH A 515 SITE 3 AC1 17 HOH A 517 HOH A 536 HOH A 560 HOH A 568 SITE 4 AC1 17 HOH A 599 HOH A 605 HOH A 644 HOH A 683 SITE 5 AC1 17 HOH A 739 SITE 1 AC2 12 ARG A 169 HIS A 170 ARG A 176 ARG A 186 SITE 2 AC2 12 ARG A 218 GLN A 271 GLY A 272 LYS A 297 SITE 3 AC2 12 HOH A 513 HOH A 542 HOH A 640 HOH A 642 SITE 1 AC3 4 ARG A 169 HOH A 503 HOH A 513 HOH A 524 SITE 1 AC4 8 THR A 162 THR A 164 ASN A 265 HOH A 516 SITE 2 AC4 8 HOH A 555 HOH A 562 HOH A 590 HOH A 746 SITE 1 AC5 3 LYS A 65 TYR A 101 GDP A 401 CRYST1 192.650 37.080 44.800 90.00 90.00 90.00 P 21 21 2 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 0.005191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.026969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022321 0.00000