HEADER HYDROLASE 18-FEB-04 1UX1 TITLE BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH A CYS53HIS AND AN ARG56GLN TITLE 2 SUBSTITUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDINE DEAMINASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: CYTIDINE AMINOHYDROLASE, CDA; COMPND 5 EC: 3.5.4.5; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: SO5201; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTRCC53H/R56QCDA KEYWDS CYTIDINE DEAMINASE, CDD, TETRAMER, ZINC BINDING, PYRIMIDINE KEYWDS 2 METABOLISM, SALVAGE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.JOHANSSON,J.NEUHARD,M.WILLEMOES,S.LARSEN REVDAT 4 13-DEC-23 1UX1 1 REMARK LINK REVDAT 3 06-MAR-19 1UX1 1 REMARK REVDAT 2 24-FEB-09 1UX1 1 VERSN REVDAT 1 20-MAY-04 1UX1 0 JRNL AUTH E.JOHANSSON,J.NEUHARD,M.WILLEMOES,S.LARSEN JRNL TITL STRUCTURAL, KINETIC, AND MUTATIONAL STUDIES OF THE ZINC ION JRNL TITL 2 ENVIRONMENT IN TETRAMERIC CYTIDINE DEAMINASE JRNL REF BIOCHEMISTRY V. 43 6020 2004 JRNL REFN ISSN 0006-2960 JRNL PMID 15147186 JRNL DOI 10.1021/BI035893X REMARK 2 REMARK 2 RESOLUTION. 2.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.66 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2004857.700 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 21345 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 SET) : 0.213 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1071 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.36 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.51 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3166 REMARK 3 BIN R VALUE (WORKING SET) : 0.2410 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 163 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3940 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 98 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.96000 REMARK 3 B22 (A**2) : -0.96000 REMARK 3 B33 (A**2) : 1.92000 REMARK 3 B12 (A**2) : 0.34000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.28 REMARK 3 ESD FROM SIGMAA (A) : 0.21 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.26 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.390 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.160 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.160 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 30.69 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER.PARAM REMARK 3 PARAMETER FILE 4 : THU_PAR REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : THU_TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1UX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 18-FEB-04. REMARK 100 THE DEPOSITION ID IS D_1290014591. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 120.0 REMARK 200 PH : 7.50 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : OSMIC MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21401 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.360 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.41 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.21700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: PDB ENTRY 1JTK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: VAPOUR DIFFUSION AT RT: PROTEIN: 4.6 REMARK 280 MG/ML, + 5 MM TETRAHYDRODEOXYURIDINE, PRECIPITANT: 30 % PEG400, REMARK 280 0.2M MAGNESIUM CHLORIDE, 0.1 M HEPES PH 7.5, PH 7.50, VAPOR REMARK 280 DIFFUSION REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 147.73600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.86800 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 73.86800 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 147.73600 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: PQS 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH B2002 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED MUTATION ARG 56 GLN IN CHAINS A B C D REMARK 400 ENGINEERED MUTATION CYS 53 HIS IN CHAINS A B C D REMARK 400 REMARK 400 THIS ENZYME SCAVENGES EXOGENOUS AND ENDOGENOUS CYTIDINE REMARK 400 AND 2'-DEOXYCYTIDINE FOR UMP SYNTHESIS. 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 132 REMARK 465 GLU A 133 REMARK 465 ARG A 134 REMARK 465 LYS A 135 REMARK 465 LEU A 136 REMARK 465 HIS B 131 REMARK 465 ASP B 132 REMARK 465 GLU B 133 REMARK 465 ARG B 134 REMARK 465 LYS B 135 REMARK 465 LEU B 136 REMARK 465 HIS C 131 REMARK 465 ASP C 132 REMARK 465 GLU C 133 REMARK 465 ARG C 134 REMARK 465 LYS C 135 REMARK 465 LEU C 136 REMARK 465 ASP D 132 REMARK 465 GLU D 133 REMARK 465 ARG D 134 REMARK 465 LYS D 135 REMARK 465 LEU D 136 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 TYR A 48 -34.93 -31.99 REMARK 500 ASN A 107 -152.06 -135.55 REMARK 500 LEU A 130 12.44 -69.80 REMARK 500 TYR B 48 -35.17 -35.36 REMARK 500 ASN B 107 -153.78 -139.56 REMARK 500 TYR C 48 -39.73 -34.80 REMARK 500 ASN C 107 -153.17 -133.34 REMARK 500 TYR D 48 -34.95 -38.21 REMARK 500 CYS D 51 135.64 -38.62 REMARK 500 GLN D 71 -30.81 -130.35 REMARK 500 LYS D 99 -7.51 -57.93 REMARK 500 ASN D 107 -158.86 -139.31 REMARK 500 GLN D 109 38.75 -144.89 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 A1132 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 53 ND1 REMARK 620 2 CYS A 86 SG 101.6 REMARK 620 3 CYS A 89 SG 113.9 120.3 REMARK 620 4 THU A 138 O4 114.7 103.9 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1131 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 53 ND1 REMARK 620 2 CYS B 86 SG 100.3 REMARK 620 3 CYS B 89 SG 112.9 117.3 REMARK 620 4 THU B 138 O4 115.9 110.2 100.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C1131 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS C 53 ND1 REMARK 620 2 CYS C 86 SG 101.7 REMARK 620 3 CYS C 89 SG 114.3 117.3 REMARK 620 4 THU C 138 O4 114.1 99.5 109.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D1132 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 53 ND1 REMARK 620 2 CYS D 86 SG 99.1 REMARK 620 3 CYS D 89 SG 114.2 120.7 REMARK 620 4 THU D 138 O4 113.3 107.9 102.1 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 A1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C1131 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D1132 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THU A 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS A1133 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THU B 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THU C 138 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE THU D 138 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JTK RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM BACILLUSSUBTILIS IN REMARK 900 COMPLEX WITH THE INHIBITOR TETRAHYDRODEOXYURIDINE REMARK 900 RELATED ID: 1UWZ RELATED DB: PDB REMARK 900 BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH AN ARG56 TO ALA REMARK 900 SUBSTITUTION REMARK 900 RELATED ID: 1UX0 RELATED DB: PDB REMARK 900 BACILLUS SUBTILIS CYTIDINE DEAMINASE WITH AN ARG56 TO GLN REMARK 900 SUBSTITUTION DBREF 1UX1 A 1 136 UNP P19079 CDD_BACSU 1 136 DBREF 1UX1 B 1 136 UNP P19079 CDD_BACSU 1 136 DBREF 1UX1 C 1 136 UNP P19079 CDD_BACSU 1 136 DBREF 1UX1 D 1 136 UNP P19079 CDD_BACSU 1 136 SEQADV 1UX1 HIS A 53 UNP P19079 CYS 53 ENGINEERED MUTATION SEQADV 1UX1 HIS B 53 UNP P19079 CYS 53 ENGINEERED MUTATION SEQADV 1UX1 HIS C 53 UNP P19079 CYS 53 ENGINEERED MUTATION SEQADV 1UX1 HIS D 53 UNP P19079 CYS 53 ENGINEERED MUTATION SEQADV 1UX1 GLN A 56 UNP P19079 ARG 56 ENGINEERED MUTATION SEQADV 1UX1 GLN B 56 UNP P19079 ARG 56 ENGINEERED MUTATION SEQADV 1UX1 GLN C 56 UNP P19079 ARG 56 ENGINEERED MUTATION SEQADV 1UX1 GLN D 56 UNP P19079 ARG 56 ENGINEERED MUTATION SEQRES 1 A 136 MET ASN ARG GLN GLU LEU ILE THR GLU ALA LEU LYS ALA SEQRES 2 A 136 ARG ASP MET ALA TYR ALA PRO TYR SER LYS PHE GLN VAL SEQRES 3 A 136 GLY ALA ALA LEU LEU THR LYS ASP GLY LYS VAL TYR ARG SEQRES 4 A 136 GLY CYS ASN ILE GLU ASN ALA ALA TYR SER MET CYS ASN SEQRES 5 A 136 HIS ALA GLU GLN THR ALA LEU PHE LYS ALA VAL SER GLU SEQRES 6 A 136 GLY ASP THR GLU PHE GLN MET LEU ALA VAL ALA ALA ASP SEQRES 7 A 136 THR PRO GLY PRO VAL SER PRO CYS GLY ALA CYS ARG GLN SEQRES 8 A 136 VAL ILE SER GLU LEU CYS THR LYS ASP VAL ILE VAL VAL SEQRES 9 A 136 LEU THR ASN LEU GLN GLY GLN ILE LYS GLU MET THR VAL SEQRES 10 A 136 GLU GLU LEU LEU PRO GLY ALA PHE SER SER GLU ASP LEU SEQRES 11 A 136 HIS ASP GLU ARG LYS LEU SEQRES 1 B 136 MET ASN ARG GLN GLU LEU ILE THR GLU ALA LEU LYS ALA SEQRES 2 B 136 ARG ASP MET ALA TYR ALA PRO TYR SER LYS PHE GLN VAL SEQRES 3 B 136 GLY ALA ALA LEU LEU THR LYS ASP GLY LYS VAL TYR ARG SEQRES 4 B 136 GLY CYS ASN ILE GLU ASN ALA ALA TYR SER MET CYS ASN SEQRES 5 B 136 HIS ALA GLU GLN THR ALA LEU PHE LYS ALA VAL SER GLU SEQRES 6 B 136 GLY ASP THR GLU PHE GLN MET LEU ALA VAL ALA ALA ASP SEQRES 7 B 136 THR PRO GLY PRO VAL SER PRO CYS GLY ALA CYS ARG GLN SEQRES 8 B 136 VAL ILE SER GLU LEU CYS THR LYS ASP VAL ILE VAL VAL SEQRES 9 B 136 LEU THR ASN LEU GLN GLY GLN ILE LYS GLU MET THR VAL SEQRES 10 B 136 GLU GLU LEU LEU PRO GLY ALA PHE SER SER GLU ASP LEU SEQRES 11 B 136 HIS ASP GLU ARG LYS LEU SEQRES 1 C 136 MET ASN ARG GLN GLU LEU ILE THR GLU ALA LEU LYS ALA SEQRES 2 C 136 ARG ASP MET ALA TYR ALA PRO TYR SER LYS PHE GLN VAL SEQRES 3 C 136 GLY ALA ALA LEU LEU THR LYS ASP GLY LYS VAL TYR ARG SEQRES 4 C 136 GLY CYS ASN ILE GLU ASN ALA ALA TYR SER MET CYS ASN SEQRES 5 C 136 HIS ALA GLU GLN THR ALA LEU PHE LYS ALA VAL SER GLU SEQRES 6 C 136 GLY ASP THR GLU PHE GLN MET LEU ALA VAL ALA ALA ASP SEQRES 7 C 136 THR PRO GLY PRO VAL SER PRO CYS GLY ALA CYS ARG GLN SEQRES 8 C 136 VAL ILE SER GLU LEU CYS THR LYS ASP VAL ILE VAL VAL SEQRES 9 C 136 LEU THR ASN LEU GLN GLY GLN ILE LYS GLU MET THR VAL SEQRES 10 C 136 GLU GLU LEU LEU PRO GLY ALA PHE SER SER GLU ASP LEU SEQRES 11 C 136 HIS ASP GLU ARG LYS LEU SEQRES 1 D 136 MET ASN ARG GLN GLU LEU ILE THR GLU ALA LEU LYS ALA SEQRES 2 D 136 ARG ASP MET ALA TYR ALA PRO TYR SER LYS PHE GLN VAL SEQRES 3 D 136 GLY ALA ALA LEU LEU THR LYS ASP GLY LYS VAL TYR ARG SEQRES 4 D 136 GLY CYS ASN ILE GLU ASN ALA ALA TYR SER MET CYS ASN SEQRES 5 D 136 HIS ALA GLU GLN THR ALA LEU PHE LYS ALA VAL SER GLU SEQRES 6 D 136 GLY ASP THR GLU PHE GLN MET LEU ALA VAL ALA ALA ASP SEQRES 7 D 136 THR PRO GLY PRO VAL SER PRO CYS GLY ALA CYS ARG GLN SEQRES 8 D 136 VAL ILE SER GLU LEU CYS THR LYS ASP VAL ILE VAL VAL SEQRES 9 D 136 LEU THR ASN LEU GLN GLY GLN ILE LYS GLU MET THR VAL SEQRES 10 D 136 GLU GLU LEU LEU PRO GLY ALA PHE SER SER GLU ASP LEU SEQRES 11 D 136 HIS ASP GLU ARG LYS LEU HET THU A 138 16 HET ZN A1132 1 HET TRS A1133 8 HET THU B 138 16 HET ZN B1131 1 HET THU C 138 16 HET ZN C1131 1 HET THU D 138 16 HET ZN D1132 1 HETNAM THU TETRAHYDRODEOXYURIDINE HETNAM ZN ZINC ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 5 THU 4(C9 H14 N2 O5) FORMUL 6 ZN 4(ZN 2+) FORMUL 7 TRS C4 H12 N O3 1+ FORMUL 14 HOH *98(H2 O) HELIX 1 1 ASN A 2 ASP A 15 1 14 HELIX 2 2 ALA A 47 CYS A 51 5 5 HELIX 3 3 HIS A 53 SER A 64 1 12 HELIX 4 4 CYS A 86 CYS A 97 1 12 HELIX 5 5 VAL A 117 LEU A 121 1 5 HELIX 6 6 SER A 126 HIS A 131 5 6 HELIX 7 7 ASN B 2 ASP B 15 1 14 HELIX 8 8 ALA B 47 CYS B 51 5 5 HELIX 9 9 HIS B 53 SER B 64 1 12 HELIX 10 10 CYS B 86 CYS B 97 1 12 HELIX 11 11 VAL B 117 LEU B 121 1 5 HELIX 12 12 SER B 126 LEU B 130 5 5 HELIX 13 13 ASN C 2 ASP C 15 1 14 HELIX 14 14 ALA C 47 CYS C 51 5 5 HELIX 15 15 HIS C 53 SER C 64 1 12 HELIX 16 16 CYS C 86 CYS C 97 1 12 HELIX 17 17 VAL C 117 LEU C 121 1 5 HELIX 18 18 SER C 126 LEU C 130 5 5 HELIX 19 19 ASN D 2 ASP D 15 1 14 HELIX 20 20 ALA D 47 CYS D 51 5 5 HELIX 21 21 HIS D 53 GLU D 65 1 13 HELIX 22 22 CYS D 86 CYS D 97 1 12 HELIX 23 23 VAL D 117 LEU D 121 1 5 HELIX 24 24 SER D 126 HIS D 131 5 6 SHEET 1 AA 5 VAL A 37 CYS A 41 0 SHEET 2 AA 5 VAL A 26 THR A 32 -1 O ALA A 28 N GLY A 40 SHEET 3 AA 5 PHE A 70 ALA A 77 -1 N GLN A 71 O LEU A 31 SHEET 4 AA 5 ILE A 102 THR A 106 1 O ILE A 102 N LEU A 73 SHEET 5 AA 5 ILE A 112 THR A 116 -1 O LYS A 113 N LEU A 105 SHEET 1 BA 5 VAL B 37 CYS B 41 0 SHEET 2 BA 5 VAL B 26 THR B 32 -1 O ALA B 28 N GLY B 40 SHEET 3 BA 5 PHE B 70 ALA B 77 -1 N GLN B 71 O LEU B 31 SHEET 4 BA 5 ILE B 102 THR B 106 1 O ILE B 102 N LEU B 73 SHEET 5 BA 5 ILE B 112 THR B 116 -1 O LYS B 113 N LEU B 105 SHEET 1 CA 5 VAL C 37 CYS C 41 0 SHEET 2 CA 5 VAL C 26 THR C 32 -1 O ALA C 28 N GLY C 40 SHEET 3 CA 5 PHE C 70 ALA C 77 -1 N GLN C 71 O LEU C 31 SHEET 4 CA 5 ILE C 102 THR C 106 1 O ILE C 102 N LEU C 73 SHEET 5 CA 5 ILE C 112 THR C 116 -1 O LYS C 113 N LEU C 105 SHEET 1 DA 5 VAL D 37 CYS D 41 0 SHEET 2 DA 5 VAL D 26 THR D 32 -1 O ALA D 28 N GLY D 40 SHEET 3 DA 5 PHE D 70 ALA D 77 -1 N GLN D 71 O LEU D 31 SHEET 4 DA 5 ILE D 102 ASN D 107 1 O ILE D 102 N LEU D 73 SHEET 5 DA 5 ILE D 112 THR D 116 -1 O LYS D 113 N LEU D 105 LINK ND1 HIS A 53 ZN ZN A1132 1555 1555 2.13 LINK SG CYS A 86 ZN ZN A1132 1555 1555 2.28 LINK SG CYS A 89 ZN ZN A1132 1555 1555 2.35 LINK O4 THU A 138 ZN ZN A1132 1555 1555 2.31 LINK ND1 HIS B 53 ZN ZN B1131 1555 1555 2.16 LINK SG CYS B 86 ZN ZN B1131 1555 1555 2.36 LINK SG CYS B 89 ZN ZN B1131 1555 1555 2.35 LINK O4 THU B 138 ZN ZN B1131 1555 1555 2.32 LINK ND1 HIS C 53 ZN ZN C1131 1555 1555 2.12 LINK SG CYS C 86 ZN ZN C1131 1555 1555 2.31 LINK SG CYS C 89 ZN ZN C1131 1555 1555 2.35 LINK O4 THU C 138 ZN ZN C1131 1555 1555 2.12 LINK ND1 HIS D 53 ZN ZN D1132 1555 1555 2.16 LINK SG CYS D 86 ZN ZN D1132 1555 1555 2.37 LINK SG CYS D 89 ZN ZN D1132 1555 1555 2.29 LINK O4 THU D 138 ZN ZN D1132 1555 1555 2.27 SITE 1 AC1 4 HIS A 53 CYS A 86 CYS A 89 THU A 138 SITE 1 AC2 4 HIS B 53 CYS B 86 CYS B 89 THU B 138 SITE 1 AC3 4 HIS C 53 CYS C 86 CYS C 89 THU C 138 SITE 1 AC4 4 HIS D 53 CYS D 86 CYS D 89 THU D 138 SITE 1 AC5 13 SER A 22 PHE A 24 VAL A 26 ASN A 42 SITE 2 AC5 13 GLU A 44 HIS A 53 ALA A 54 GLU A 55 SITE 3 AC5 13 PRO A 85 CYS A 86 CYS A 89 ZN A1132 SITE 4 AC5 13 ALA C 46 SITE 1 AC6 5 ASP A 15 ALA A 17 GLN A 25 ASP C 15 SITE 2 AC6 5 GLN C 25 SITE 1 AC7 13 SER B 22 PHE B 24 VAL B 26 ASN B 42 SITE 2 AC7 13 GLU B 44 HIS B 53 ALA B 54 GLU B 55 SITE 3 AC7 13 PRO B 85 CYS B 86 CYS B 89 ZN B1131 SITE 4 AC7 13 ALA D 46 SITE 1 AC8 15 ALA A 46 ALA A 47 TYR A 48 PHE C 24 SITE 2 AC8 15 VAL C 26 ASN C 42 GLU C 44 HIS C 53 SITE 3 AC8 15 ALA C 54 GLU C 55 PRO C 85 CYS C 86 SITE 4 AC8 15 CYS C 89 ZN C1131 PHE D 125 SITE 1 AC9 14 ALA B 46 ALA B 47 TYR B 48 PHE D 24 SITE 2 AC9 14 VAL D 26 ASN D 42 GLU D 44 HIS D 53 SITE 3 AC9 14 ALA D 54 GLU D 55 PRO D 85 CYS D 86 SITE 4 AC9 14 CYS D 89 ZN D1132 CRYST1 62.484 62.484 221.604 90.00 90.00 120.00 P 32 2 1 24 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 0.016004 0.009240 0.000000 0.00000 SCALE2 0.000000 0.018480 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004512 0.00000 MTRIX1 1 0.260457 0.954156 0.147471 -7.08630 1 MTRIX2 1 0.953530 -0.278176 0.115750 -18.56337 1 MTRIX3 1 0.151467 0.110470 -0.982270 178.45891 1 MTRIX1 2 -0.980847 0.004784 -0.194722 62.99423 1 MTRIX2 2 0.011362 -0.996591 -0.081720 28.70962 1 MTRIX3 2 -0.194449 -0.082367 0.977448 7.33272 1 MTRIX1 3 -0.286679 -0.957326 0.036628 36.29831 1 MTRIX2 3 -0.956970 0.284359 -0.057860 34.82265 1 MTRIX3 3 0.044975 -0.051639 -0.997653 183.99223 1