HEADER HYDROLASE 09-MAY-17 5XKQ TITLE CRYSTAL STRUCTURE OF MSMEG3575 IN COMPLEX WITH AMMELINE 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 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, CDA FOLD, DEAMINASE, AMMELINE EXPDTA X-RAY DIFFRACTION AUTHOR V.M.GADED,R.ANAND REVDAT 3 22-NOV-23 5XKQ 1 LINK REVDAT 2 16-AUG-17 5XKQ 1 JRNL REVDAT 1 09-AUG-17 5XKQ 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. 2.70 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 109.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 17737 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.500 REMARK 3 FREE R VALUE TEST SET COUNT : 832 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 886 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.04 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 56 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.05000 REMARK 3 B33 (A**2) : 0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.03000 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): 0.363 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.268 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.221 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4786 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4371 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6537 ; 1.452 ; 1.929 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9927 ; 1.421 ; 2.999 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 611 ; 5.726 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 200 ;37.365 ;22.300 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 626 ;15.372 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;19.169 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 734 ; 0.078 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5490 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1131 ; 0.007 ; 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): 2469 ; 3.124 ; 4.428 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2467 ; 3.124 ; 4.427 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3071 ; 4.848 ; 6.627 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3072 ; 4.848 ; 6.628 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2317 ; 3.293 ; 4.788 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2318 ; 3.292 ; 4.787 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3467 ; 5.246 ; 7.058 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5217 ; 7.720 ;36.259 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5217 ; 7.712 ;36.259 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 16488 0.11 0.05 REMARK 3 2 A 2 159 C 2 159 17118 0.05 0.05 REMARK 3 3 A 2 159 D 2 159 16484 0.10 0.05 REMARK 3 4 B 2 159 C 2 159 16284 0.11 0.05 REMARK 3 5 B 2 159 D 2 159 17980 0.03 0.05 REMARK 3 6 C 2 159 D 2 159 16286 0.10 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 : 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 5XKQ 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_1300003716. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-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 : 19362 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 109.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.75 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 (%): 50.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 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, HANGING REMARK 280 DROP, TEMPERATURE 290K 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 30.69600 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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: 2750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -64.0 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 MET A 1 REMARK 465 VAL A 48 REMARK 465 LYS A 49 REMARK 465 ASP A 50 REMARK 465 GLY A 51 REMARK 465 MET B 1 REMARK 465 LYS B 49 REMARK 465 ASP B 50 REMARK 465 GLY B 51 REMARK 465 MET C 1 REMARK 465 VAL C 48 REMARK 465 LYS C 49 REMARK 465 ASP C 50 REMARK 465 MET D 1 REMARK 465 LYS D 49 REMARK 465 ASP D 50 REMARK 465 GLY D 51 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 GLU A 20 CG CD OE1 OE2 REMARK 470 ASP A 35 CG OD1 OD2 REMARK 470 ARG A 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 73 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 144 CG CD OE1 OE2 REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 ARG B 67 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 LYS C 9 CG CD CE NZ REMARK 470 GLU C 20 CG CD OE1 OE2 REMARK 470 ASP C 24 CG OD1 OD2 REMARK 470 ASP C 35 CG OD1 OD2 REMARK 470 ARG C 63 CZ NH1 NH2 REMARK 470 ARG C 67 CG CD NE CZ NH1 NH2 REMARK 470 ARG C 73 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 144 CG CD OE1 OE2 REMARK 470 GLU C 147 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 ARG D 67 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 143 CG CD OE1 OE2 REMARK 470 GLU D 147 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 O CYS A 14 O HOH A 301 2.13 REMARK 500 OD1 ASP D 35 OG1 THR D 37 2.19 REMARK 500 OD1 ASP B 35 OG1 THR B 37 2.19 REMARK 500 N GLY A 30 O HOH A 301 2.19 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 24 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ASP A 52 CB - CG - OD1 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 52 CB - CG - OD2 ANGL. DEV. = -7.4 DEGREES REMARK 500 ASP C 52 CB - CG - OD1 ANGL. DEV. = 6.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG B 47 46.90 -145.78 REMARK 500 ARG D 47 46.54 -145.19 REMARK 500 PRO D 71 -39.05 -39.21 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 ALA A 2 ILE A 3 146.67 REMARK 500 ALA C 2 ILE C 3 146.77 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 56 ND1 REMARK 620 2 CYS A 86 SG 109.0 REMARK 620 3 CYS A 89 SG 110.1 119.0 REMARK 620 4 HOH A 307 O 113.3 111.9 92.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 56 ND1 REMARK 620 2 CYS B 86 SG 109.7 REMARK 620 3 CYS B 89 SG 110.0 120.0 REMARK 620 4 HOH B 305 O 104.3 114.3 97.0 REMARK 620 N 1 2 3 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 109.3 REMARK 620 3 CYS C 89 SG 110.1 120.4 REMARK 620 4 HOH C 304 O 109.5 111.0 95.5 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 108.8 REMARK 620 3 CYS D 89 SG 109.5 119.8 REMARK 620 4 HOH D 308 O 98.7 114.9 103.0 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 ZN A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6AM A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6AM B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6AM C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6AM D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 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: 5XKP RELATED DB: PDB REMARK 900 RELATED ID: 5XKR RELATED DB: PDB DBREF 5XKQ A 1 159 UNP A0QY90 A0QY90_MYCS2 1 159 DBREF 5XKQ B 1 159 UNP A0QY90 A0QY90_MYCS2 1 159 DBREF 5XKQ C 1 159 UNP A0QY90 A0QY90_MYCS2 1 159 DBREF 5XKQ D 1 159 UNP A0QY90 A0QY90_MYCS2 1 159 SEQRES 1 A 159 MET ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG SEQRES 2 A 159 CYS VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP SEQRES 3 A 159 GLU PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR SEQRES 4 A 159 THR LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP SEQRES 5 A 159 ALA THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA SEQRES 6 A 159 ALA ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR SEQRES 7 A 159 VAL TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA SEQRES 8 A 159 ALA HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA SEQRES 9 A 159 THR SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP SEQRES 10 A 159 GLY ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN SEQRES 11 A 159 THR VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU SEQRES 12 A 159 GLU LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS SEQRES 13 A 159 PHE GLY ARG SEQRES 1 B 159 MET ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG SEQRES 2 B 159 CYS VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP SEQRES 3 B 159 GLU PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR SEQRES 4 B 159 THR LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP SEQRES 5 B 159 ALA THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA SEQRES 6 B 159 ALA ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR SEQRES 7 B 159 VAL TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA SEQRES 8 B 159 ALA HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA SEQRES 9 B 159 THR SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP SEQRES 10 B 159 GLY ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN SEQRES 11 B 159 THR VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU SEQRES 12 B 159 GLU LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS SEQRES 13 B 159 PHE GLY ARG SEQRES 1 C 159 MET ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG SEQRES 2 C 159 CYS VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP SEQRES 3 C 159 GLU PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR SEQRES 4 C 159 THR LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP SEQRES 5 C 159 ALA THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA SEQRES 6 C 159 ALA ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR SEQRES 7 C 159 VAL TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA SEQRES 8 C 159 ALA HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA SEQRES 9 C 159 THR SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP SEQRES 10 C 159 GLY ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN SEQRES 11 C 159 THR VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU SEQRES 12 C 159 GLU LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS SEQRES 13 C 159 PHE GLY ARG SEQRES 1 D 159 MET ALA ILE SER ASP ALA ASP LEU LYS TYR LEU ARG ARG SEQRES 2 D 159 CYS VAL ASP LEU ALA ARG GLU ALA LEU ASP ASP GLY ASP SEQRES 3 D 159 GLU PRO PHE GLY SER VAL LEU VAL ASP HIS THR GLY THR SEQRES 4 D 159 THR LEU PHE GLU ASP ARG ASN ARG VAL LYS ASP GLY ASP SEQRES 5 D 159 ALA THR ALA HIS PRO GLU PHE ALA ILE ALA ARG TRP ALA SEQRES 6 D 159 ALA ARG HIS LEU THR PRO ASP ARG ARG ALA ARG ALA THR SEQRES 7 D 159 VAL TYR THR SER GLY GLU HIS CYS PRO MET CYS ALA ALA SEQRES 8 D 159 ALA HIS ALA TRP VAL GLY LEU GLY ARG ILE VAL TYR ALA SEQRES 9 D 159 THR SER SER ALA GLN LEU GLY GLY TRP LEU THR GLU TRP SEQRES 10 D 159 GLY ALA GLN ALA PRO PRO VAL ALA THR LEU PRO ILE ASN SEQRES 11 D 159 THR VAL ALA PRO GLY VAL VAL VAL ASP GLY PRO ALA GLU SEQRES 12 D 159 GLU LEU ALA GLU THR MET HIS ASN LEU TYR ARG ALA LYS SEQRES 13 D 159 PHE GLY ARG HET ZN A 201 1 HET 6AM A 202 9 HET ZN B 201 1 HET 6AM B 202 9 HET GOL B 203 6 HET 6AM C 201 9 HET ZN C 202 1 HET 6AM D 201 9 HET ZN D 202 1 HET GOL D 203 6 HET ACT D 204 4 HETNAM ZN ZINC ION HETNAM 6AM 4,6-DIAMINO-1,3,5-TRIAZIN-2-OL HETNAM GOL GLYCEROL HETNAM ACT ACETATE ION HETSYN 6AM AMMELINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 ZN 4(ZN 2+) FORMUL 6 6AM 4(C3 H5 N5 O) FORMUL 9 GOL 2(C3 H8 O3) FORMUL 15 ACT C2 H3 O2 1- FORMUL 16 HOH *34(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 GLY A 97 1 12 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 LEU A 41 SHEET 3 AA1 5 THR A 78 GLY A 83 -1 O THR A 78 N VAL A 34 SHEET 4 AA1 5 ILE A 101 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 LEU B 41 SHEET 3 AA2 5 THR B 78 GLY B 83 -1 O THR B 78 N VAL B 34 SHEET 4 AA2 5 ILE B 101 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 LEU C 41 SHEET 3 AA3 5 THR C 78 GLY C 83 -1 O THR C 78 N VAL C 34 SHEET 4 AA3 5 ILE C 101 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 LEU D 41 SHEET 3 AA4 5 THR D 78 GLY D 83 -1 O THR D 78 N VAL D 34 SHEET 4 AA4 5 ILE D 101 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 201 1555 1555 2.14 LINK SG CYS A 86 ZN L ZN A 201 1555 1555 2.31 LINK SG CYS A 89 ZN L ZN A 201 1555 1555 2.34 LINK ZN L ZN A 201 O HOH A 307 1555 1555 2.01 LINK ND1 HIS B 56 ZN L ZN B 201 1555 1555 2.15 LINK SG CYS B 86 ZN L ZN B 201 1555 1555 2.28 LINK SG CYS B 89 ZN L ZN B 201 1555 1555 2.32 LINK ZN L ZN B 201 O HOH B 305 1555 1555 2.02 LINK ND1 HIS C 56 ZN L ZN C 202 1555 1555 2.16 LINK SG CYS C 86 ZN L ZN C 202 1555 1555 2.31 LINK SG CYS C 89 ZN L ZN C 202 1555 1555 2.32 LINK ZN L ZN C 202 O HOH C 304 1555 1555 2.01 LINK ND1 HIS D 56 ZN L ZN D 202 1555 1555 2.17 LINK SG CYS D 86 ZN L ZN D 202 1555 1555 2.29 LINK SG CYS D 89 ZN L ZN D 202 1555 1555 2.31 LINK ZN L ZN D 202 O HOH D 308 1555 1555 2.00 CISPEP 1 GLY A 140 PRO A 141 0 5.43 CISPEP 2 GLY B 140 PRO B 141 0 4.80 CISPEP 3 GLY C 140 PRO C 141 0 6.39 CISPEP 4 GLY D 140 PRO D 141 0 4.60 SITE 1 AC1 4 HIS A 56 CYS A 86 CYS A 89 HOH A 307 SITE 1 AC2 7 GLU A 27 PHE A 29 ASN A 46 HIS A 56 SITE 2 AC2 7 CYS A 86 HOH A 307 TRP B 95 SITE 1 AC3 4 HIS B 56 CYS B 86 CYS B 89 HOH B 305 SITE 1 AC4 7 TRP A 95 GLU B 27 PHE B 29 ASN B 46 SITE 2 AC4 7 HIS B 56 CYS B 86 HOH B 305 SITE 1 AC5 3 ARG B 19 THR B 148 ASN B 151 SITE 1 AC6 7 GLU C 27 PHE C 29 ASN C 46 HIS C 56 SITE 2 AC6 7 CYS C 86 HOH C 304 TRP D 95 SITE 1 AC7 4 HIS C 56 CYS C 86 CYS C 89 HOH C 304 SITE 1 AC8 8 TRP C 95 GLU D 27 PHE D 29 ASN D 46 SITE 2 AC8 8 HIS D 56 CYS D 86 GOL D 203 HOH D 308 SITE 1 AC9 4 HIS D 56 CYS D 86 CYS D 89 HOH D 308 SITE 1 AD1 2 GLN D 120 6AM D 201 SITE 1 AD2 3 ARG D 19 THR D 148 ASN D 151 CRYST1 52.679 61.392 109.406 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 0.018983 0.000000 -0.000018 0.00000 SCALE2 0.000000 0.016289 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009140 0.00000