HEADER HYDROLASE 09-MAY-12 4F3W TITLE CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE CDD FROM MYCOBACTERIUM MARINUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDINE DEAMINASE CDD; COMPND 3 CHAIN: A, B, C, D; COMPND 4 EC: 3.5.4.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM MARINUM; SOURCE 3 ORGANISM_TAXID: 216594; SOURCE 4 STRAIN: ATCC BAA-535 / M; SOURCE 5 GENE: CDD, MMAR_1204; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PAVA0421 KEYWDS STRUCTURAL GENOMICS, NIAID, NATIONAL INSTITUTE OF ALLERGY AND KEYWDS 2 INFECTIOUS DISEASES, SEATTLE STRUCTURAL GENOMICS CENTER FOR KEYWDS 3 INFECTIOUS DISEASE, SSGCID, MYCOBACTERIUM, ORTHOLOG, CYTIDINE, KEYWDS 4 URIDINE, ZINC BINDING ENZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE (SSGCID) REVDAT 4 13-SEP-23 4F3W 1 REMARK SEQADV LINK REVDAT 3 15-APR-15 4F3W 1 JRNL REVDAT 2 11-MAR-15 4F3W 1 JRNL REVDAT 1 23-MAY-12 4F3W 0 JRNL AUTH L.BAUGH,I.PHAN,D.W.BEGLEY,M.C.CLIFTON,B.ARMOUR,D.M.DRANOW, JRNL AUTH 2 B.M.TAYLOR,M.M.MURUTHI,J.ABENDROTH,J.W.FAIRMAN,D.FOX, JRNL AUTH 3 S.H.DIETERICH,B.L.STAKER,A.S.GARDBERG,R.CHOI,S.N.HEWITT, JRNL AUTH 4 A.J.NAPULI,J.MYERS,L.K.BARRETT,Y.ZHANG,M.FERRELL,E.MUNDT, JRNL AUTH 5 K.THOMPKINS,N.TRAN,S.LYONS-ABBOTT,A.ABRAMOV,A.SEKAR, JRNL AUTH 6 D.SERBZHINSKIY,D.LORIMER,G.W.BUCHKO,R.STACY,L.J.STEWART, JRNL AUTH 7 T.E.EDWARDS,W.C.VAN VOORHIS,P.J.MYLER JRNL TITL INCREASING THE STRUCTURAL COVERAGE OF TUBERCULOSIS DRUG JRNL TITL 2 TARGETS. JRNL REF TUBERCULOSIS (EDINB) V. 95 142 2015 JRNL REFN ISSN 1472-9792 JRNL PMID 25613812 JRNL DOI 10.1016/J.TUBE.2014.12.003 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 39960 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) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1977 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2726 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.2170 REMARK 3 BIN FREE R VALUE SET COUNT : 130 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3437 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 299 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.40000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.08000 REMARK 3 B12 (A**2) : 0.31000 REMARK 3 B13 (A**2) : 0.42000 REMARK 3 B23 (A**2) : 0.04000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.133 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.126 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.082 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.229 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3518 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2345 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4800 ; 1.478 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5694 ; 0.941 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 481 ; 5.514 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 134 ;29.730 ;22.239 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;13.433 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;15.459 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 546 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4068 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 718 ; 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): 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 : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 4 A 122 REMARK 3 RESIDUE RANGE : A 201 A 201 REMARK 3 RESIDUE RANGE : A 301 A 373 REMARK 3 ORIGIN FOR THE GROUP (A): 0.5229 -5.5335 -20.0100 REMARK 3 T TENSOR REMARK 3 T11: 0.0309 T22: 0.0276 REMARK 3 T33: 0.0525 T12: 0.0017 REMARK 3 T13: 0.0286 T23: -0.0028 REMARK 3 L TENSOR REMARK 3 L11: 0.4730 L22: 0.4082 REMARK 3 L33: 1.0391 L12: -0.2219 REMARK 3 L13: -0.2086 L23: -0.4300 REMARK 3 S TENSOR REMARK 3 S11: -0.0876 S12: -0.0101 S13: -0.0326 REMARK 3 S21: 0.0300 S22: 0.0556 S23: 0.0107 REMARK 3 S31: 0.0693 S32: -0.0555 S33: 0.0320 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 122 REMARK 3 RESIDUE RANGE : B 201 B 201 REMARK 3 RESIDUE RANGE : B 301 B 379 REMARK 3 ORIGIN FOR THE GROUP (A): 3.0335 3.4655 -40.7792 REMARK 3 T TENSOR REMARK 3 T11: 0.0126 T22: 0.0653 REMARK 3 T33: 0.0408 T12: -0.0047 REMARK 3 T13: -0.0086 T23: -0.0331 REMARK 3 L TENSOR REMARK 3 L11: 0.9376 L22: 0.1872 REMARK 3 L33: 1.2736 L12: -0.2316 REMARK 3 L13: -0.8051 L23: -0.0565 REMARK 3 S TENSOR REMARK 3 S11: -0.0453 S12: 0.1849 S13: -0.0117 REMARK 3 S21: 0.0308 S22: -0.0235 S23: -0.0451 REMARK 3 S31: 0.0169 S32: -0.1703 S33: 0.0688 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 4 C 122 REMARK 3 RESIDUE RANGE : C 201 C 201 REMARK 3 RESIDUE RANGE : C 301 C 372 REMARK 3 ORIGIN FOR THE GROUP (A): 21.9284 17.1536 -30.2317 REMARK 3 T TENSOR REMARK 3 T11: 0.0245 T22: 0.0177 REMARK 3 T33: 0.0442 T12: 0.0029 REMARK 3 T13: 0.0008 T23: 0.0138 REMARK 3 L TENSOR REMARK 3 L11: 0.6669 L22: 0.2616 REMARK 3 L33: 0.7010 L12: -0.1248 REMARK 3 L13: -0.3457 L23: -0.2020 REMARK 3 S TENSOR REMARK 3 S11: 0.0468 S12: 0.0007 S13: 0.0474 REMARK 3 S21: -0.0155 S22: -0.0401 S23: -0.0081 REMARK 3 S31: 0.0242 S32: 0.0287 S33: -0.0066 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : D 3 D 122 REMARK 3 RESIDUE RANGE : D 201 D 201 REMARK 3 RESIDUE RANGE : D 301 D 375 REMARK 3 ORIGIN FOR THE GROUP (A): 9.0020 16.6500 -11.3739 REMARK 3 T TENSOR REMARK 3 T11: 0.0580 T22: 0.0113 REMARK 3 T33: 0.0184 T12: 0.0119 REMARK 3 T13: -0.0155 T23: -0.0003 REMARK 3 L TENSOR REMARK 3 L11: 0.4089 L22: 0.4497 REMARK 3 L33: 0.9896 L12: -0.1365 REMARK 3 L13: -0.0246 L23: -0.3751 REMARK 3 S TENSOR REMARK 3 S11: -0.0168 S12: 0.0085 S13: -0.0227 REMARK 3 S21: 0.0702 S22: 0.0325 S23: -0.0190 REMARK 3 S31: -0.0603 S32: -0.0158 S33: -0.0157 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: U VALUES : WITH TLS ADDED HYDROGENS REMARK 3 HAVE BEEN ADDED IN THE RIDING POSITIONS REMARK 4 REMARK 4 4F3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000072422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39961 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.980 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.3.0 REMARK 200 STARTING MODEL: PDB ENTRY 3IJF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.43 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MYMAA.00495.A.A1 PS00823 AT 20 MG/ML REMARK 280 AGAINST JCSG+ A8 0.2 M SODIUM FORMATE, 20% PEG 3350, CRYSTAL REMARK 280 TRACKING ID 232847A8, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 289K, PH 7 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -219.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 GLY A -3 REMARK 465 PRO A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 PRO A 2 REMARK 465 ASP A 3 REMARK 465 PHE A 123 REMARK 465 HIS A 124 REMARK 465 ALA A 125 REMARK 465 ASP A 126 REMARK 465 LEU A 127 REMARK 465 THR A 128 REMARK 465 GLY A 129 REMARK 465 GLU A 130 REMARK 465 PRO A 131 REMARK 465 GLY B -3 REMARK 465 PRO B -2 REMARK 465 GLY B -1 REMARK 465 SER B 0 REMARK 465 MET B 1 REMARK 465 PHE B 123 REMARK 465 HIS B 124 REMARK 465 ALA B 125 REMARK 465 ASP B 126 REMARK 465 LEU B 127 REMARK 465 THR B 128 REMARK 465 GLY B 129 REMARK 465 GLU B 130 REMARK 465 PRO B 131 REMARK 465 GLY C -3 REMARK 465 PRO C -2 REMARK 465 GLY C -1 REMARK 465 SER C 0 REMARK 465 MET C 1 REMARK 465 PRO C 2 REMARK 465 ASP C 3 REMARK 465 PHE C 123 REMARK 465 HIS C 124 REMARK 465 ALA C 125 REMARK 465 ASP C 126 REMARK 465 LEU C 127 REMARK 465 THR C 128 REMARK 465 GLY C 129 REMARK 465 GLU C 130 REMARK 465 PRO C 131 REMARK 465 GLY D -3 REMARK 465 PRO D -2 REMARK 465 GLY D -1 REMARK 465 SER D 0 REMARK 465 MET D 1 REMARK 465 PRO D 2 REMARK 465 PHE D 123 REMARK 465 HIS D 124 REMARK 465 ALA D 125 REMARK 465 ASP D 126 REMARK 465 LEU D 127 REMARK 465 THR D 128 REMARK 465 GLY D 129 REMARK 465 GLU D 130 REMARK 465 PRO D 131 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 7 CG CD CE NZ REMARK 470 GLN A 8 CG CD OE1 NE2 REMARK 470 ARG A 26 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 ASP B 3 CG OD1 OD2 REMARK 470 LYS B 7 CG CD CE NZ REMARK 470 ARG B 82 CG CD NE CZ NH1 NH2 REMARK 470 GLU C 121 CG CD OE1 OE2 REMARK 470 ASP D 3 CG OD1 OD2 REMARK 470 LYS D 7 CG CD CE NZ REMARK 470 LYS D 12 CG CD CE NZ REMARK 470 GLN D 15 CG CD OE1 NE2 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 HIS A 66 CG HIS A 66 CD2 0.056 REMARK 500 HIS D 99 CG HIS D 99 CD2 0.057 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 110 -29.82 86.48 REMARK 500 ALA C 110 -30.61 85.98 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 CYS A 56 SG REMARK 620 2 CYS A 89 SG 119.6 REMARK 620 3 CYS A 92 SG 103.4 113.8 REMARK 620 4 HOH A 323 O 108.3 105.8 105.0 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 CYS B 56 SG REMARK 620 2 CYS B 89 SG 118.8 REMARK 620 3 CYS B 92 SG 102.1 117.4 REMARK 620 4 HOH B 325 O 109.3 104.3 104.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 56 SG REMARK 620 2 CYS C 89 SG 118.5 REMARK 620 3 CYS C 92 SG 101.3 114.7 REMARK 620 4 HOH C 335 O 109.2 107.1 105.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 56 SG REMARK 620 2 CYS D 89 SG 118.7 REMARK 620 3 CYS D 92 SG 102.0 113.7 REMARK 620 4 HOH D 328 O 111.0 105.8 105.0 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 ZN B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IJF RELATED DB: PDB REMARK 900 CYTIDINE DEAMINASE FROM M. TUBERCULOSIS REMARK 900 RELATED ID: 3R2N RELATED DB: PDB REMARK 900 CYTIDINE DEAMINASE FROM M. LEPRAE REMARK 900 RELATED ID: 3MPZ RELATED DB: PDB REMARK 900 CYTIDINE DEAMINASE FROM M. SMEGMATIS REMARK 900 RELATED ID: MYMAA.00495.A RELATED DB: TARGETTRACK DBREF 4F3W A 1 131 UNP B2HDU6 B2HDU6_MYCMM 1 131 DBREF 4F3W B 1 131 UNP B2HDU6 B2HDU6_MYCMM 1 131 DBREF 4F3W C 1 131 UNP B2HDU6 B2HDU6_MYCMM 1 131 DBREF 4F3W D 1 131 UNP B2HDU6 B2HDU6_MYCMM 1 131 SEQADV 4F3W GLY A -3 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W PRO A -2 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W GLY A -1 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W SER A 0 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W GLY B -3 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W PRO B -2 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W GLY B -1 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W SER B 0 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W GLY C -3 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W PRO C -2 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W GLY C -1 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W SER C 0 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W GLY D -3 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W PRO D -2 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W GLY D -1 UNP B2HDU6 EXPRESSION TAG SEQADV 4F3W SER D 0 UNP B2HDU6 EXPRESSION TAG SEQRES 1 A 135 GLY PRO GLY SER MET PRO ASP ILE ASP TRP LYS GLN LEU SEQRES 2 A 135 ARG ASP LYS ALA THR GLN VAL ALA ALA GLY ALA TYR ALA SEQRES 3 A 135 PRO TYR SER ARG PHE PRO VAL GLY ALA ALA ALA LEU VAL SEQRES 4 A 135 ASP ASP GLY ARG VAL VAL THR GLY CYS ASN VAL GLU ASN SEQRES 5 A 135 VAL SER TYR GLY LEU ALA LEU CYS ALA GLU CYS GLY VAL SEQRES 6 A 135 VAL CYS ALA LEU HIS ALA THR GLY GLY GLY ARG LEU VAL SEQRES 7 A 135 ALA LEU ALA CYS VAL ASP GLY ARG GLY ALA PRO LEU MET SEQRES 8 A 135 PRO CYS GLY ARG CYS ARG GLN LEU LEU PHE GLU HIS GLY SEQRES 9 A 135 GLY PRO GLU LEU LEU VAL ASP HIS LEU ALA GLY PRO ARG SEQRES 10 A 135 ARG LEU GLY ASP LEU LEU PRO GLU PRO PHE HIS ALA ASP SEQRES 11 A 135 LEU THR GLY GLU PRO SEQRES 1 B 135 GLY PRO GLY SER MET PRO ASP ILE ASP TRP LYS GLN LEU SEQRES 2 B 135 ARG ASP LYS ALA THR GLN VAL ALA ALA GLY ALA TYR ALA SEQRES 3 B 135 PRO TYR SER ARG PHE PRO VAL GLY ALA ALA ALA LEU VAL SEQRES 4 B 135 ASP ASP GLY ARG VAL VAL THR GLY CYS ASN VAL GLU ASN SEQRES 5 B 135 VAL SER TYR GLY LEU ALA LEU CYS ALA GLU CYS GLY VAL SEQRES 6 B 135 VAL CYS ALA LEU HIS ALA THR GLY GLY GLY ARG LEU VAL SEQRES 7 B 135 ALA LEU ALA CYS VAL ASP GLY ARG GLY ALA PRO LEU MET SEQRES 8 B 135 PRO CYS GLY ARG CYS ARG GLN LEU LEU PHE GLU HIS GLY SEQRES 9 B 135 GLY PRO GLU LEU LEU VAL ASP HIS LEU ALA GLY PRO ARG SEQRES 10 B 135 ARG LEU GLY ASP LEU LEU PRO GLU PRO PHE HIS ALA ASP SEQRES 11 B 135 LEU THR GLY GLU PRO SEQRES 1 C 135 GLY PRO GLY SER MET PRO ASP ILE ASP TRP LYS GLN LEU SEQRES 2 C 135 ARG ASP LYS ALA THR GLN VAL ALA ALA GLY ALA TYR ALA SEQRES 3 C 135 PRO TYR SER ARG PHE PRO VAL GLY ALA ALA ALA LEU VAL SEQRES 4 C 135 ASP ASP GLY ARG VAL VAL THR GLY CYS ASN VAL GLU ASN SEQRES 5 C 135 VAL SER TYR GLY LEU ALA LEU CYS ALA GLU CYS GLY VAL SEQRES 6 C 135 VAL CYS ALA LEU HIS ALA THR GLY GLY GLY ARG LEU VAL SEQRES 7 C 135 ALA LEU ALA CYS VAL ASP GLY ARG GLY ALA PRO LEU MET SEQRES 8 C 135 PRO CYS GLY ARG CYS ARG GLN LEU LEU PHE GLU HIS GLY SEQRES 9 C 135 GLY PRO GLU LEU LEU VAL ASP HIS LEU ALA GLY PRO ARG SEQRES 10 C 135 ARG LEU GLY ASP LEU LEU PRO GLU PRO PHE HIS ALA ASP SEQRES 11 C 135 LEU THR GLY GLU PRO SEQRES 1 D 135 GLY PRO GLY SER MET PRO ASP ILE ASP TRP LYS GLN LEU SEQRES 2 D 135 ARG ASP LYS ALA THR GLN VAL ALA ALA GLY ALA TYR ALA SEQRES 3 D 135 PRO TYR SER ARG PHE PRO VAL GLY ALA ALA ALA LEU VAL SEQRES 4 D 135 ASP ASP GLY ARG VAL VAL THR GLY CYS ASN VAL GLU ASN SEQRES 5 D 135 VAL SER TYR GLY LEU ALA LEU CYS ALA GLU CYS GLY VAL SEQRES 6 D 135 VAL CYS ALA LEU HIS ALA THR GLY GLY GLY ARG LEU VAL SEQRES 7 D 135 ALA LEU ALA CYS VAL ASP GLY ARG GLY ALA PRO LEU MET SEQRES 8 D 135 PRO CYS GLY ARG CYS ARG GLN LEU LEU PHE GLU HIS GLY SEQRES 9 D 135 GLY PRO GLU LEU LEU VAL ASP HIS LEU ALA GLY PRO ARG SEQRES 10 D 135 ARG LEU GLY ASP LEU LEU PRO GLU PRO PHE HIS ALA ASP SEQRES 11 D 135 LEU THR GLY GLU PRO HET ZN A 201 1 HET ZN B 201 1 HET ZN C 201 1 HET ZN D 201 1 HETNAM ZN ZINC ION FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *299(H2 O) HELIX 1 1 ASP A 5 ALA A 18 1 14 HELIX 2 2 SER A 50 ALA A 54 5 5 HELIX 3 3 CYS A 56 THR A 68 1 13 HELIX 4 4 CYS A 89 GLY A 101 1 13 HELIX 5 5 LEU A 115 LEU A 119 1 5 HELIX 6 6 ASP B 5 ALA B 18 1 14 HELIX 7 7 SER B 50 ALA B 54 5 5 HELIX 8 8 CYS B 56 THR B 68 1 13 HELIX 9 9 CYS B 89 GLY B 101 1 13 HELIX 10 10 LEU B 115 LEU B 119 1 5 HELIX 11 11 ASP C 5 ALA C 18 1 14 HELIX 12 12 SER C 50 ALA C 54 5 5 HELIX 13 13 CYS C 56 THR C 68 1 13 HELIX 14 14 CYS C 89 GLY C 101 1 13 HELIX 15 15 LEU C 115 LEU C 119 1 5 HELIX 16 16 ASP D 5 ALA D 17 1 13 HELIX 17 17 ALA D 18 ALA D 20 5 3 HELIX 18 18 SER D 50 ALA D 54 5 5 HELIX 19 19 CYS D 56 THR D 68 1 13 HELIX 20 20 CYS D 89 GLY D 101 1 13 HELIX 21 21 LEU D 115 LEU D 119 1 5 SHEET 1 A 5 VAL A 40 CYS A 44 0 SHEET 2 A 5 GLY A 30 VAL A 35 -1 N ALA A 33 O VAL A 41 SHEET 3 A 5 LEU A 73 VAL A 79 -1 O VAL A 74 N LEU A 34 SHEET 4 A 5 LEU A 105 VAL A 106 1 O LEU A 105 N LEU A 76 SHEET 5 A 5 ARG A 113 ARG A 114 -1 O ARG A 113 N VAL A 106 SHEET 1 B 5 VAL B 40 CYS B 44 0 SHEET 2 B 5 VAL B 29 VAL B 35 -1 N ALA B 33 O VAL B 41 SHEET 3 B 5 LEU B 73 ASP B 80 -1 O VAL B 74 N LEU B 34 SHEET 4 B 5 LEU B 105 VAL B 106 1 O LEU B 105 N LEU B 76 SHEET 5 B 5 ARG B 113 ARG B 114 -1 O ARG B 113 N VAL B 106 SHEET 1 C 5 VAL C 40 CYS C 44 0 SHEET 2 C 5 GLY C 30 VAL C 35 -1 N ALA C 33 O VAL C 41 SHEET 3 C 5 LEU C 73 VAL C 79 -1 O VAL C 74 N LEU C 34 SHEET 4 C 5 LEU C 105 VAL C 106 1 O LEU C 105 N LEU C 76 SHEET 5 C 5 ARG C 113 ARG C 114 -1 O ARG C 113 N VAL C 106 SHEET 1 D 5 VAL D 40 CYS D 44 0 SHEET 2 D 5 VAL D 29 VAL D 35 -1 N ALA D 33 O VAL D 41 SHEET 3 D 5 LEU D 73 ASP D 80 -1 O VAL D 74 N LEU D 34 SHEET 4 D 5 LEU D 105 VAL D 106 1 O LEU D 105 N LEU D 76 SHEET 5 D 5 ARG D 113 ARG D 114 -1 O ARG D 113 N VAL D 106 LINK SG CYS A 56 ZN ZN A 201 1555 1555 2.32 LINK SG CYS A 89 ZN ZN A 201 1555 1555 2.34 LINK SG CYS A 92 ZN ZN A 201 1555 1555 2.37 LINK ZN ZN A 201 O HOH A 323 1555 1555 2.04 LINK SG CYS B 56 ZN ZN B 201 1555 1555 2.38 LINK SG CYS B 89 ZN ZN B 201 1555 1555 2.34 LINK SG CYS B 92 ZN ZN B 201 1555 1555 2.32 LINK ZN ZN B 201 O HOH B 325 1555 1555 2.14 LINK SG CYS C 56 ZN ZN C 201 1555 1555 2.39 LINK SG CYS C 89 ZN ZN C 201 1555 1555 2.34 LINK SG CYS C 92 ZN ZN C 201 1555 1555 2.28 LINK ZN ZN C 201 O HOH C 335 1555 1555 2.16 LINK SG CYS D 56 ZN ZN D 201 1555 1555 2.42 LINK SG CYS D 89 ZN ZN D 201 1555 1555 2.32 LINK SG CYS D 92 ZN ZN D 201 1555 1555 2.34 LINK ZN ZN D 201 O HOH D 328 1555 1555 2.06 SITE 1 AC1 4 CYS A 56 CYS A 89 CYS A 92 HOH A 323 SITE 1 AC2 4 CYS B 56 CYS B 89 CYS B 92 HOH B 325 SITE 1 AC3 4 CYS C 56 CYS C 89 CYS C 92 HOH C 335 SITE 1 AC4 4 CYS D 56 CYS D 89 CYS D 92 HOH D 328 CRYST1 47.470 48.710 53.920 100.19 110.42 98.39 P 1 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 0.021066 0.003106 0.008877 0.00000 SCALE2 0.000000 0.020752 0.005261 0.00000 SCALE3 0.000000 0.000000 0.020415 0.00000