HEADER HYDROLASE 08-MAY-17 5XKP TITLE CRYSTAL STRUCTURE OF MSMEG3575 IN COMPLEX WITH 5-AZACYTOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CMP/DCMP DEAMINASE, ZINC-BINDING PROTEIN; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: CYTIDINE/DEOXYCYTIDYLATE DEAMINASE,ZINC-BINDING REGION; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: 5-AZACYTOSINE IS USED AS A CHEMOTHERAPEUTIC DRUG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 3 MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 GENE: MSMEG_3575, MSMEI_3493; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 10 EXPRESSION_SYSTEM_CELL_LINE: BL21 DE3; SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS HYDROLASE, DEAMINASE, CDA FOLD, 5-AZACYTOSINE EXPDTA X-RAY DIFFRACTION AUTHOR V.M.GADED,R.ANAND REVDAT 3 22-NOV-23 5XKP 1 LINK REVDAT 2 16-AUG-17 5XKP 1 JRNL REVDAT 1 09-AUG-17 5XKP 0 JRNL AUTH V.GADED,R.ANAND JRNL TITL SELECTIVE DEAMINATION OF MUTAGENS BY A MYCOBACTERIAL ENZYME JRNL REF J. AM. CHEM. SOC. V. 139 10762 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28708393 JRNL DOI 10.1021/JACS.7B04967 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 62.08 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 12845 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.242 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 653 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 725 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE SET COUNT : 29 REMARK 3 BIN FREE R VALUE : 0.3540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4664 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 64 REMARK 3 SOLVENT ATOMS : 32 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.79 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.05000 REMARK 3 B22 (A**2) : -0.06000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.457 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.344 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.998 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.944 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4837 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4395 ; 0.010 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6607 ; 1.568 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10028 ; 1.846 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 624 ; 5.977 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 204 ;39.202 ;22.549 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 631 ;17.852 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;15.174 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 740 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5582 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1146 ; 0.011 ; 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): 2515 ; 3.333 ; 5.945 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2513 ; 3.331 ; 5.943 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3132 ; 5.291 ; 8.905 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3133 ; 5.290 ; 8.906 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2322 ; 3.211 ; 6.138 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2323 ; 3.211 ; 6.138 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3476 ; 5.004 ; 9.123 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 21393 ;10.259 ;56.492 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 21393 ;10.259 ;56.492 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 2 159 B 2 159 16396 0.13 0.05 REMARK 3 2 A 2 159 C 2 159 17258 0.07 0.05 REMARK 3 3 A 2 159 D 2 159 16228 0.13 0.05 REMARK 3 4 B 2 159 C 2 159 16112 0.13 0.05 REMARK 3 5 B 2 159 D 2 159 17764 0.07 0.05 REMARK 3 6 C 2 159 D 2 159 15996 0.13 0.05 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5XKP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1300003715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 - 7.0 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) : 0.98 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 : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 13940 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 62.080 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10600 REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 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: 5XKO REMARK 200 REMARK 200 REMARK: FLAT PLATE LIKE CRYSTALS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M MAGNESIUM ACETATE TETRAHYDRATE, REMARK 280 0.1 M TRIS-HCL (PH 6.4) AND 20% PEG 8000, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K 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 54.41550 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: 2950 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 3110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D 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 ASP A 50 REMARK 465 ASP C 50 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 ASP A 5 CG OD1 OD2 REMARK 470 LYS A 9 CG CD CE NZ REMARK 470 LYS A 49 CG CD CE NZ REMARK 470 ARG A 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 THR B 39 OG1 CG2 REMARK 470 ASP B 50 CG OD1 OD2 REMARK 470 ARG B 67 CG CD NE CZ NH1 NH2 REMARK 470 ASP B 72 CG OD1 OD2 REMARK 470 ARG B 76 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 143 CG CD OE1 OE2 REMARK 470 GLU B 147 OE2 REMARK 470 ARG B 159 CG CD NE CZ NH1 NH2 REMARK 470 ILE C 3 CG1 CG2 CD1 REMARK 470 LYS C 9 CG CD CE NZ REMARK 470 ARG C 12 CG CD NE CZ NH1 NH2 REMARK 470 LYS C 49 CB CG CD CE NZ REMARK 470 ARG C 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 76 CG CD NE CZ NH1 NH2 REMARK 470 GLN C 120 CG CD OE1 NE2 REMARK 470 GLU C 143 CG CD OE1 OE2 REMARK 470 ARG C 159 CG CD NE CZ NH1 NH2 REMARK 470 LYS D 9 CG CD CE NZ REMARK 470 THR D 37 OG1 CG2 REMARK 470 THR D 39 OG1 CG2 REMARK 470 ASP D 50 CG OD1 OD2 REMARK 470 ARG D 67 CG CD NE CZ NH1 NH2 REMARK 470 THR D 70 OG1 CG2 REMARK 470 ASP D 72 CG OD1 OD2 REMARK 470 ARG D 76 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 143 CG CD OE1 OE2 REMARK 470 ARG D 159 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 ZN ZN D 202 O HOH D 301 1.42 REMARK 500 OD1 ASP B 35 CG2 THR B 37 1.55 REMARK 500 ZN ZN B 202 O HOH B 301 1.61 REMARK 500 N7 5AZ B 201 O HOH B 301 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 307 O HOH B 307 2444 2.07 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 B 44 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG C 45 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 GLY D 38 N - CA - C ANGL. DEV. = 15.0 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 ARG A 47 41.54 -140.60 REMARK 500 GLU A 84 132.82 -37.23 REMARK 500 ASP B 50 -13.75 -47.69 REMARK 500 GLU B 84 132.94 -37.55 REMARK 500 ARG C 47 42.69 -140.56 REMARK 500 GLU C 84 132.17 -37.55 REMARK 500 THR D 37 48.37 -80.50 REMARK 500 GLU D 84 133.06 -37.49 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 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 56 ND1 REMARK 620 2 CYS A 86 SG 116.7 REMARK 620 3 CYS A 89 SG 101.0 130.5 REMARK 620 4 HOH A 302 O 90.8 118.2 90.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 56 ND1 REMARK 620 2 CYS B 86 SG 117.6 REMARK 620 3 CYS B 89 SG 106.4 125.1 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 56 ND1 REMARK 620 2 CYS C 86 SG 116.4 REMARK 620 3 CYS C 89 SG 106.5 130.9 REMARK 620 4 HOH C 302 O 97.7 102.8 93.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 56 ND1 REMARK 620 2 CYS D 86 SG 111.6 REMARK 620 3 CYS D 89 SG 110.6 127.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5AZ A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5AZ B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5AZ C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 5AZ D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT D 204 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5XKO RELATED DB: PDB REMARK 900 RELATED ID: 5XKQ RELATED DB: PDB REMARK 900 RELATED ID: 5XKR RELATED DB: PDB DBREF 5XKP A 2 159 UNP A0QY90 A0QY90_MYCS2 2 159 DBREF 5XKP B 2 159 UNP A0QY90 A0QY90_MYCS2 2 159 DBREF 5XKP C 2 159 UNP A0QY90 A0QY90_MYCS2 2 159 DBREF 5XKP D 2 159 UNP A0QY90 A0QY90_MYCS2 2 159 SEQRES 1 A 158 ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG CYS SEQRES 2 A 158 VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP GLU SEQRES 3 A 158 PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR THR SEQRES 4 A 158 LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP ALA SEQRES 5 A 158 THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA ALA SEQRES 6 A 158 ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR VAL SEQRES 7 A 158 TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA ALA SEQRES 8 A 158 HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA THR SEQRES 9 A 158 SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP GLY SEQRES 10 A 158 ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN THR SEQRES 11 A 158 VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU GLU SEQRES 12 A 158 LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS PHE SEQRES 13 A 158 GLY ARG SEQRES 1 B 158 ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG CYS SEQRES 2 B 158 VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP GLU SEQRES 3 B 158 PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR THR SEQRES 4 B 158 LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP ALA SEQRES 5 B 158 THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA ALA SEQRES 6 B 158 ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR VAL SEQRES 7 B 158 TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA ALA SEQRES 8 B 158 HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA THR SEQRES 9 B 158 SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP GLY SEQRES 10 B 158 ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN THR SEQRES 11 B 158 VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU GLU SEQRES 12 B 158 LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS PHE SEQRES 13 B 158 GLY ARG SEQRES 1 C 158 ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG CYS SEQRES 2 C 158 VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP GLU SEQRES 3 C 158 PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR THR SEQRES 4 C 158 LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP ALA SEQRES 5 C 158 THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA ALA SEQRES 6 C 158 ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR VAL SEQRES 7 C 158 TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA ALA SEQRES 8 C 158 HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA THR SEQRES 9 C 158 SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP GLY SEQRES 10 C 158 ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN THR SEQRES 11 C 158 VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU GLU SEQRES 12 C 158 LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS PHE SEQRES 13 C 158 GLY ARG SEQRES 1 D 158 ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG CYS SEQRES 2 D 158 VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP GLU SEQRES 3 D 158 PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR THR SEQRES 4 D 158 LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP ALA SEQRES 5 D 158 THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA ALA SEQRES 6 D 158 ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR VAL SEQRES 7 D 158 TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA ALA SEQRES 8 D 158 HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA THR SEQRES 9 D 158 SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP GLY SEQRES 10 D 158 ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN THR SEQRES 11 D 158 VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU GLU SEQRES 12 D 158 LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS PHE SEQRES 13 D 158 GLY ARG HET 5AZ A 201 8 HET ZN A 202 1 HET GOL A 203 6 HET 5AZ B 201 8 HET ZN B 202 1 HET GOL B 203 6 HET 5AZ C 201 8 HET ZN C 202 1 HET GOL C 203 6 HET 5AZ D 201 8 HET ZN D 202 1 HET GOL D 203 6 HET ACT D 204 4 HETNAM 5AZ 6-AMINO-1,3,5-TRIAZIN-2(1H)-ONE HETNAM ZN ZINC ION HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN 5AZ 5-AZACYTOSINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 5AZ 4(C3 H4 N4 O) FORMUL 6 ZN 4(ZN 2+) FORMUL 7 GOL 4(C3 H8 O3) FORMUL 17 ACT C2 H3 O2 1- FORMUL 18 HOH *32(H2 O) HELIX 1 AA1 SER A 4 ASP A 24 1 21 HELIX 2 AA2 HIS A 56 LEU A 69 1 14 HELIX 3 AA3 THR A 70 ALA A 77 1 8 HELIX 4 AA4 CYS A 86 VAL A 96 1 11 HELIX 5 AA5 SER A 106 TRP A 117 1 12 HELIX 6 AA6 PRO A 128 ALA A 133 1 6 HELIX 7 AA7 ALA A 142 GLU A 144 5 3 HELIX 8 AA8 LEU A 145 GLY A 158 1 14 HELIX 9 AA9 SER B 4 ASP B 24 1 21 HELIX 10 AB1 HIS B 56 LEU B 69 1 14 HELIX 11 AB2 THR B 70 ALA B 77 1 8 HELIX 12 AB3 CYS B 86 VAL B 96 1 11 HELIX 13 AB4 SER B 106 TRP B 117 1 12 HELIX 14 AB5 PRO B 128 ALA B 133 1 6 HELIX 15 AB6 ALA B 142 GLU B 144 5 3 HELIX 16 AB7 LEU B 145 GLY B 158 1 14 HELIX 17 AB8 SER C 4 ASP C 24 1 21 HELIX 18 AB9 HIS C 56 LEU C 69 1 14 HELIX 19 AC1 THR C 70 ALA C 77 1 8 HELIX 20 AC2 CYS C 86 VAL C 96 1 11 HELIX 21 AC3 SER C 106 TRP C 117 1 12 HELIX 22 AC4 PRO C 128 ALA C 133 1 6 HELIX 23 AC5 ALA C 142 GLU C 144 5 3 HELIX 24 AC6 LEU C 145 GLY C 158 1 14 HELIX 25 AC7 SER D 4 ASP D 24 1 21 HELIX 26 AC8 HIS D 56 LEU D 69 1 14 HELIX 27 AC9 THR D 70 ALA D 77 1 8 HELIX 28 AD1 CYS D 86 VAL D 96 1 11 HELIX 29 AD2 SER D 106 TRP D 117 1 12 HELIX 30 AD3 PRO D 128 ALA D 133 1 6 HELIX 31 AD4 ALA D 142 GLU D 144 5 3 HELIX 32 AD5 LEU D 145 GLY D 158 1 14 SHEET 1 AA1 5 THR A 40 ARG A 45 0 SHEET 2 AA1 5 GLY A 30 VAL A 34 -1 N LEU A 33 O PHE A 42 SHEET 3 AA1 5 THR A 78 GLY A 83 -1 O THR A 78 N VAL A 34 SHEET 4 AA1 5 ARG A 100 THR A 105 1 O VAL A 102 N VAL A 79 SHEET 5 AA1 5 VAL A 138 ASP A 139 1 O ASP A 139 N ILE A 101 SHEET 1 AA2 5 THR B 40 ARG B 45 0 SHEET 2 AA2 5 GLY B 30 VAL B 34 -1 N LEU B 33 O PHE B 42 SHEET 3 AA2 5 THR B 78 GLY B 83 -1 O SER B 82 N GLY B 30 SHEET 4 AA2 5 ARG B 100 THR B 105 1 O VAL B 102 N VAL B 79 SHEET 5 AA2 5 VAL B 138 ASP B 139 1 O ASP B 139 N ILE B 101 SHEET 1 AA3 5 THR C 40 ARG C 45 0 SHEET 2 AA3 5 GLY C 30 VAL C 34 -1 N LEU C 33 O PHE C 42 SHEET 3 AA3 5 THR C 78 GLY C 83 -1 O THR C 78 N VAL C 34 SHEET 4 AA3 5 ARG C 100 THR C 105 1 O VAL C 102 N VAL C 79 SHEET 5 AA3 5 VAL C 138 ASP C 139 1 O ASP C 139 N ILE C 101 SHEET 1 AA4 5 THR D 40 ARG D 45 0 SHEET 2 AA4 5 GLY D 30 VAL D 34 -1 N LEU D 33 O PHE D 42 SHEET 3 AA4 5 THR D 78 GLY D 83 -1 O SER D 82 N GLY D 30 SHEET 4 AA4 5 ARG D 100 THR D 105 1 O VAL D 102 N VAL D 79 SHEET 5 AA4 5 VAL D 138 ASP D 139 1 O ASP D 139 N ILE D 101 LINK ND1 HIS A 56 ZN L ZN A 202 1555 1555 2.16 LINK SG CYS A 86 ZN L ZN A 202 1555 1555 2.18 LINK SG CYS A 89 ZN L ZN A 202 1555 1555 2.33 LINK ZN L ZN A 202 O HOH A 302 1555 1555 1.81 LINK ND1 HIS B 56 ZN L ZN B 202 1555 1555 2.03 LINK SG CYS B 86 ZN L ZN B 202 1555 1555 2.26 LINK SG CYS B 89 ZN L ZN B 202 1555 1555 2.34 LINK ND1 HIS C 56 ZN L ZN C 202 1555 1555 2.07 LINK SG CYS C 86 ZN L ZN C 202 1555 1555 2.23 LINK SG CYS C 89 ZN L ZN C 202 1555 1555 2.26 LINK ZN L ZN C 202 O HOH C 302 1555 1555 1.91 LINK ND1 HIS D 56 ZN L ZN D 202 1555 1555 2.08 LINK SG CYS D 86 ZN L ZN D 202 1555 1555 2.35 LINK SG CYS D 89 ZN L ZN D 202 1555 1555 2.20 CISPEP 1 GLY A 140 PRO A 141 0 -5.03 CISPEP 2 GLY B 140 PRO B 141 0 0.55 CISPEP 3 GLY C 140 PRO C 141 0 -2.46 CISPEP 4 GLY D 140 PRO D 141 0 0.48 SITE 1 AC1 9 PHE A 29 ASN A 46 HIS A 56 GLU A 58 SITE 2 AC1 9 GLU A 84 HIS A 85 CYS A 86 GOL A 203 SITE 3 AC1 9 HOH A 302 SITE 1 AC2 4 HIS A 56 CYS A 86 CYS A 89 HOH A 302 SITE 1 AC3 3 GLU A 27 GLN A 120 5AZ A 201 SITE 1 AC4 9 PHE B 29 ASN B 46 HIS B 56 PRO B 57 SITE 2 AC4 9 GLU B 58 GLU B 84 CYS B 86 ZN B 202 SITE 3 AC4 9 HOH B 301 SITE 1 AC5 5 HIS B 56 CYS B 86 CYS B 89 5AZ B 201 SITE 2 AC5 5 HOH B 301 SITE 1 AC6 3 GLU B 27 GLN B 120 PHE B 157 SITE 1 AC7 8 PHE C 29 ASN C 46 HIS C 56 GLU C 58 SITE 2 AC7 8 GLU C 84 CYS C 86 GOL C 203 HOH C 302 SITE 1 AC8 4 HIS C 56 CYS C 86 CYS C 89 HOH C 302 SITE 1 AC9 3 GLU C 27 PRO C 122 5AZ C 201 SITE 1 AD1 10 PHE D 29 ASN D 46 HIS D 56 PRO D 57 SITE 2 AD1 10 GLU D 58 GLU D 84 CYS D 86 ZN D 202 SITE 3 AD1 10 GOL D 203 HOH D 301 SITE 1 AD2 5 HIS D 56 CYS D 86 CYS D 89 5AZ D 201 SITE 2 AD2 5 HOH D 301 SITE 1 AD3 3 GLU D 27 PHE D 157 5AZ D 201 SITE 1 AD4 2 VAL D 138 GLY D 140 CRYST1 52.621 108.831 62.076 90.00 89.95 90.00 P 1 21 1 8 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 0.019004 0.000000 -0.000015 0.00000 SCALE2 0.000000 0.009189 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016109 0.00000