10 20 30 40 50 60 70 80 5GGA - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 15-JUN-16 5GGA
TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM SMEGMATIS MUTT1 IN COMPLEX WITH 8- TITLE 2 OXO-GDP, 8-OXO-GMP AND PYROPHOSPHATE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROLASE, NUDIX FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MUTT1; COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS STR. 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 8-OXO-GUANINE NUCLEOTIDES, SANITIZATION OF NUCLEOTIDE POOL, NUDIX KEYWDS 2 ENZYME, HISTIDINE PHOSPHATASE DOMAIN, BINDING SITES AT KEYWDS 3 INTERMOLECULAR INTERFACE, ENZYME ACTION, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR S.M.ARIF,A.G.PATIL,U.VARSHNEY,M.VIJAYAN
REVDAT 1 19-APR-17 5GGA 0
JRNL AUTH S.M.ARIF,A.G.PATIL,U.VARSHNEY,M.VIJAYAN JRNL TITL BIOCHEMICAL AND STRUCTURAL STUDIES OF MYCOBACTERIUM JRNL TITL 2 SMEGMATIS MUTT1, A SANITIZATION ENZYME WITH UNUSUAL MODES OF JRNL TITL 3 ASSOCIATION JRNL REF ACTA CRYSTALLOGR D STRUCT V. 73 349 2017 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 28375146 JRNL DOI 10.1107/S2059798317002534
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.M.ARIF,A.G.PATIL,U.VARSHNEY,M.VIJAYAN REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF MUTT1 REMARK 1 TITL 2 (MSMEG_2390) FROM MYCOBACTERIUM SMEGMATIS REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 68 1214 2012 REMARK 1 REFN ESSN 1744-3091 REMARK 1 PMID 23027750 REMARK 1 DOI 10.1107/S1744309112035804
REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 28782 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) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1533 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2088 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3260 REMARK 3 BIN FREE R VALUE SET COUNT : 123 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2305 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.69000 REMARK 3 B22 (A**2) : -1.85000 REMARK 3 B33 (A**2) : 3.28000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.121 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.124 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.115 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.913 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2475 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2328 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3384 ; 2.008 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5352 ; 0.882 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 301 ; 6.766 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 114 ;33.904 ;22.544 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 404 ;15.598 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;17.875 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 364 ; 0.117 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2772 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 557 ; 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): 1195 ; 3.057 ; 3.297 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1194 ; 3.055 ; 3.295 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1499 ; 4.056 ; 4.928 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1500 ; 4.055 ; 4.930 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1280 ; 4.024 ; 3.817 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1269 ; 4.036 ; 3.822 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1867 ; 5.834 ; 5.547 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3009 ; 7.508 ;28.425 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2921 ; 7.462 ;28.033 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 5GGA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1300000724.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30343 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 43.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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: 3FJY REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 TRIS HYDROCHLORIDE, 30% W/V PEG 4000, PH 8.5, MICROBATCH, REMARK 280 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 42.15000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13910 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 ALA A 35 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 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 21 CG CD CE NZ
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 154 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 3.7 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 46 45.43 -106.58 REMARK 500 ALA A 173 44.19 -145.66 REMARK 500 ASP A 183 66.74 87.36 REMARK 500 ASP A 215 54.06 -66.25 REMARK 500 THR A 270 -157.53 -140.89 REMARK 500 ASN A 295 36.49 -165.14 REMARK 500 PRO A 318 152.53 -48.96 REMARK 500 PRO A 318 152.53 -48.73 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 181 ASP A 182 -147.21 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 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 65 O REMARK 620 2 GLU A 85 OE2 95.6 REMARK 620 3 HOH A 570 O 76.6 74.5 REMARK 620 4 HOH A 650 O 164.0 71.9 90.2 REMARK 620 5 HOH A 691 O 97.8 81.6 154.7 90.3 REMARK 620 6 HOH A 566 O 101.9 162.5 109.9 91.0 95.4 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 G8D A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8GM A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue POP A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 404
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5GG5 RELATED DB: PDB REMARK 900 RELATED ID: 5GG6 RELATED DB: PDB REMARK 900 RELATED ID: 5GG7 RELATED DB: PDB REMARK 900 RELATED ID: 5GG8 RELATED DB: PDB REMARK 900 RELATED ID: 5GG9 RELATED DB: PDB REMARK 900 RELATED ID: 5GGB RELATED DB: PDB REMARK 900 RELATED ID: 5GGC RELATED DB: PDB REMARK 900 RELATED ID: 5GGD RELATED DB: PDB
DBREF 5GGA A 1 322 UNP A0QUZ2 A0QUZ2_MYCS2 1 322
SEQADV 5GGA MET A -19 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA GLY A -18 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA SER A -17 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA SER A -16 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA HIS A -15 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA HIS A -14 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA HIS A -13 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA HIS A -12 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA HIS A -11 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA HIS A -10 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA SER A -9 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA SER A -8 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA GLY A -7 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA LEU A -6 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA VAL A -5 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA PRO A -4 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA ARG A -3 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA GLY A -2 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA SER A -1 UNP A0QUZ2 EXPRESSION TAG SEQADV 5GGA 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 G8D A 401 29 HET 8GM A 402 25 HET POP A 403 9 HET MG A 404 1
HETNAM G8D [(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7- HETNAM 2 G8D DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 3 G8D PHOSPHONO HYDROGEN PHOSPHATE HETNAM 8GM [(2R,3S,4R,5R)-5-[2-AZANYL-6,8-BIS(OXIDANYLIDENE)-1,7- HETNAM 2 8GM DIHYDROPURIN-9-YL]-3,4-BIS(OXIDANYL)OXOLAN-2-YL]METHYL HETNAM 3 8GM DIHYDROGEN PHOSPHATE HETNAM POP PYROPHOSPHATE 2- HETNAM MG MAGNESIUM ION
HETSYN G8D 8-OXOGUANOSINE-5'-DIPHOSPHATE HETSYN 8GM 8-OXOGUANOSINE-5'-PHOSPHATE
FORMUL 2 G8D C10 H15 N5 O12 P2 FORMUL 3 8GM C10 H14 N5 O9 P FORMUL 4 POP H2 O7 P2 2- FORMUL 5 MG MG 2+ FORMUL 6 HOH *238(H2 O)
HELIX 1 AA1 THR A 73 GLY A 87 1 15 HELIX 2 AA2 VAL A 136 LEU A 143 1 8 HELIX 3 AA3 TYR A 145 ARG A 158 1 14 HELIX 4 AA4 ASP A 189 ALA A 205 1 17 HELIX 5 AA5 ARG A 216 ASP A 231 1 16 HELIX 6 AA6 PRO A 238 LEU A 240 5 3 HELIX 7 AA7 THR A 241 ASP A 248 1 8 HELIX 8 AA8 ASP A 248 ARG A 262 1 15 HELIX 9 AA9 VAL A 274 ALA A 286 1 13
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 ARG A 33 O GLU A 49 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 GLU A 49 N ARG A 33 SHEET 4 AA2 4 LYS A 130 PRO A 135 -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 ILE A 268 SHEET 5 AA3 6 THR A 300 SER A 306 -1 O TRP A 301 N VAL A 167 SHEET 6 AA3 6 GLU A 309 LEU A 316 -1 O LEU A 316 N THR A 300
LINK O LYS A 65 MG MG A 404 1555 1555 2.28 LINK OE2 GLU A 85 MG MG A 404 1555 1555 2.65 LINK MG MG A 404 O HOH A 570 1555 1555 2.44 LINK MG MG A 404 O HOH A 650 1555 1555 2.29 LINK MG MG A 404 O HOH A 691 1555 1555 2.18 LINK MG MG A 404 O HOH A 566 1555 1555 2.32
CISPEP 1 LYS A 21 HIS A 22 0 -8.06
SITE 1 AC1 15 ARG A 55 ARG A 57 TYR A 58 ASP A 60 SITE 2 AC1 15 SER A 62 LYS A 65 TYR A 101 LYS A 108 SITE 3 AC1 15 TYR A 145 ASP A 148 HOH A 512 HOH A 528 SITE 4 AC1 15 HOH A 532 HOH A 566 HOH A 586 SITE 1 AC2 10 ASP A 59 TRP A 61 ASP A 141 GLN A 142 SITE 2 AC2 10 GLN A 144 HOH A 506 HOH A 508 HOH A 530 SITE 3 AC2 10 HOH A 556 HOH A 582 SITE 1 AC3 12 ARG A 169 HIS A 170 ARG A 176 ARG A 186 SITE 2 AC3 12 ARG A 218 GLN A 271 GLY A 272 LYS A 297 SITE 3 AC3 12 HOH A 515 HOH A 522 HOH A 539 HOH A 551 SITE 1 AC4 6 LYS A 65 GLU A 85 HOH A 566 HOH A 570 SITE 2 AC4 6 HOH A 650 HOH A 691
CRYST1 41.730 84.300 43.580 90.00 94.01 90.00 P 1 21 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 0.023964 0.000000 0.001680 0.00000
SCALE2 0.000000 0.011862 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023003 0.00000