10 20 30 40 50 60 70 80 1R5T - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 13-OCT-03 1R5T
TITLE THE CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE CDD1, AN ORPHAN TITLE 2 C TO U EDITASE FROM YEAST
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
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: CDD1P; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODONPLUS(TM); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A
KEYWDS ZINC DEPENDENT DEAMINASE, RNA EDITING, APOBEC-1 RELATED KEYWDS 2 PROTEIN, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.XIE,M.P.SOWDEN,G.S.C.DANCE,A.T.TORELLI,H.C.SMITH, AUTHOR 2 J.E.WEDEKIND
REVDAT 2 24-FEB-09 1R5T 1 VERSN REVDAT 1 25-MAY-04 1R5T 0
JRNL AUTH K.XIE,M.P.SOWDEN,G.S.DANCE,A.T.TORELLI,H.C.SMITH, JRNL AUTH 2 J.E.WEDEKIND JRNL TITL THE STRUCTURE OF A YEAST RNA-EDITING DEAMINASE JRNL TITL 2 PROVIDES INSIGHT INTO THE FOLD AND FUNCTION OF JRNL TITL 3 ACTIVATION-INDUCED DEAMINASE AND APOBEC-1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 8114 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 15148397 JRNL DOI 10.1073/PNAS.0400493101
REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.C.SMITH,A.BOTTARO,M.P.SOWDEN,J.E.WEDEKIND REMARK 1 TITL ACTIVATION INDUCED DEAMINASE: THE IMPORTANCE OF REMARK 1 TITL 2 BEING SPECIFIC REMARK 1 REF TRENDS GENET. V. 20 224 2004 REMARK 1 REFN ISSN 0168-9525 REMARK 1 DOI 10.1016/J.TIG.2004.03.012 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.E.WEDEKIND,G.S.DANCE,M.P.SOWDEN,H.C.SMITH REMARK 1 TITL MESSENGER RNA EDITING IN MAMMALS: NEW MEMBERS OF REMARK 1 TITL 2 THE APOBEC FAMILY SEEKING ROLES IN THE FAMILY REMARK 1 TITL 3 BUSINESS REMARK 1 REF TRENDS GENET. V. 19 207 2003 REMARK 1 REFN ISSN 0168-9525 REMARK 1 DOI 10.1016/S0168-9525(03)00054-4 REMARK 1 REFERENCE 3 REMARK 1 AUTH G.S.DANCE,P.BEEMILLER,Y.YANG,D.V.MATER,I.S.MIAN, REMARK 1 AUTH 2 H.C.SMITH REMARK 1 TITL IDENTIFICATION OF THE YEAST CYTIDINE DEAMINASE REMARK 1 TITL 2 CDD1 AS AN ORPHAN C-TO-U RNA EDITASE REMARK 1 REF NUCLEIC ACIDS RES. V. 29 1772 2001 REMARK 1 REFN ISSN 0305-1048 REMARK 1 DOI 10.1093/NAR/29.8.1772 REMARK 1 REFERENCE 4 REMARK 1 AUTH G.S.DANCE,M.P.SOWDEN,Y.YANG,H.C.SMITH REMARK 1 TITL APOBEC-1 DEPENDENT CYTIDINE TO URIDINE EDITING OF REMARK 1 TITL 2 APOLIPOPROTEIN B RNA IN YEAST REMARK 1 REF NUCLEIC ACIDS RES. V. 28 424 2000 REMARK 1 REFN ISSN 0305-1048 REMARK 1 DOI 10.1093/NAR/28.2.424
REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.05 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 410906.600 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 63560 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) : 0.188 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.900 REMARK 3 FREE R VALUE TEST SET COUNT : 5026 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5991 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2800 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 512 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.012 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4195 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 318 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.21000 REMARK 3 B22 (A**2) : 2.82000 REMARK 3 B33 (A**2) : -5.03000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.18 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.20 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.72 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) : 1.350 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.750 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.280 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.990 ; 3.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.32 REMARK 3 BSOL : 41.97 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_REP.PARAM REMARK 3 PARAMETER FILE 4 : 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1R5T COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-OCT-03. REMARK 100 THE RCSB ID CODE IS RCSB020473.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-SEP-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2574, 1.2831, 1.2828 REMARK 200 MONOCHROMATOR : SI-111 REMARK 200 OPTICS : VERTICAL FOCUSING MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : APS-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63560 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE/RESOLVE, SHELXM, DM, O REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000 MME, AMMONIUM CHLORIDE, REMARK 280 SODIUM SUCCINATE, DTT, SODIUM AZIDE, PH 5.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.13000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.13000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 39.26000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.18500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.26000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.18500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 78.13000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.26000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.18500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 78.13000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.26000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.18500 REMARK 290 SMTRY3 8 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 300 REMARK: CDD1 IS A TETRAMER OF IDENTICAL SUBUNITS RELATED BY 222 REMARK 300 SYMMETRY. THE ASYMMETRIC UNIT COMPRISES 1 TETRAMER OF CHAINS A, REMARK 300 B,C AND D AND INCLUDES FOUR ZINC ATOMS.
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: 10490 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -234.0 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 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 C 180 LIES ON A SPECIAL POSITION.
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 HIS B 140 REMARK 465 LEU B 141 REMARK 465 ASN B 142 REMARK 465 MET C 1 REMARK 465 ASN C 142 REMARK 465 MET D 1 REMARK 465 LYS D 2 REMARK 465 GLY D 137 REMARK 465 PRO D 138 REMARK 465 SER D 139 REMARK 465 HIS D 140 REMARK 465 LEU D 141 REMARK 465 ASN D 142
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 HOH B 154 O HOH B 188 2.12 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 ASN A 142 N - CA - C ANGL. DEV. = 17.9 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 VAL A 3 102.53 56.04 REMARK 500 ASP A 87 33.90 -73.29 REMARK 500 ASP A 90 -61.97 -98.36 REMARK 500 SER B 77 -176.49 -174.07 REMARK 500 VAL C 3 77.05 68.50 REMARK 500 TYR C 29 -63.44 -98.63 REMARK 500 ASN C 42 30.23 -96.35 REMARK 500 ASP C 90 -69.36 -96.89 REMARK 500 ASP D 87 32.20 -88.17 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 157 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH B 158 DISTANCE = 5.61 ANGSTROMS REMARK 525 HOH C 161 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH C 163 DISTANCE = 5.78 ANGSTROMS REMARK 525 HOH B 163 DISTANCE = 5.33 ANGSTROMS REMARK 525 HOH C 164 DISTANCE = 5.37 ANGSTROMS REMARK 525 HOH C 173 DISTANCE = 5.91 ANGSTROMS REMARK 525 HOH C 180 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH B 181 DISTANCE = 6.32 ANGSTROMS REMARK 525 HOH B 184 DISTANCE = 7.17 ANGSTROMS REMARK 525 HOH A 187 DISTANCE = 8.24 ANGSTROMS REMARK 525 HOH B 199 DISTANCE = 6.22 ANGSTROMS REMARK 525 HOH A 219 DISTANCE = 6.76 ANGSTROMS REMARK 525 HOH C 221 DISTANCE = 7.07 ANGSTROMS REMARK 525 HOH A 220 DISTANCE = 8.80 ANGSTROMS REMARK 525 HOH C 224 DISTANCE = 5.76 ANGSTROMS REMARK 525 HOH C 227 DISTANCE = 5.75 ANGSTROMS REMARK 525 HOH B 231 DISTANCE = 12.33 ANGSTROMS
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 150 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 CYS A 96 SG 114.8 REMARK 620 3 CYS A 99 SG 102.9 121.8 REMARK 620 4 HOH A 223 O 105.7 103.3 107.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 151 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 61 SG REMARK 620 2 CYS B 96 SG 115.3 REMARK 620 3 CYS B 99 SG 103.8 119.5 REMARK 620 4 HOH B 209 O 109.3 104.2 103.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 152 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 61 SG REMARK 620 2 CYS C 96 SG 114.9 REMARK 620 3 CYS C 99 SG 98.5 121.0 REMARK 620 4 HOH C 198 O 103.7 109.6 107.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 153 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 61 SG REMARK 620 2 CYS D 96 SG 113.4 REMARK 620 3 CYS D 99 SG 102.5 116.7 REMARK 620 4 HOH D 179 O 108.8 102.0 113.5 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 150 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 151 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 152 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 153
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AF2 RELATED DB: PDB REMARK 900 DIMERIC CRYSTAL STRUCTURE OF BACTERIAL CYTIDINE DEAMINASE REMARK 900 COMPLEXED WITH URIDINE REMARK 900 RELATED ID: 1JTK RELATED DB: PDB REMARK 900 TETRAMERIC CRYSTAL STRUCTURE OF BACTERIAL CYTIDINE REMARK 900 DEAMINASE FROM BACILLUS SUBTILIS IN COMPLEX WITH THE REMARK 900 INHIBITOR TETRAHYDRODEOXYURIDINE
DBREF 1R5T A 1 142 UNP Q06549 CDD_YEAST 1 142 DBREF 1R5T B 1 142 UNP Q06549 CDD_YEAST 1 142 DBREF 1R5T C 1 142 UNP Q06549 CDD_YEAST 1 142 DBREF 1R5T D 1 142 UNP Q06549 CDD_YEAST 1 142
SEQRES 1 A 142 MET LYS VAL GLY GLY ILE GLU ASP ARG GLN LEU GLU ALA SEQRES 2 A 142 LEU LYS ARG ALA ALA LEU LYS ALA CYS GLU LEU SER TYR SEQRES 3 A 142 SER PRO TYR SER HIS PHE ARG VAL GLY CYS SER ILE LEU SEQRES 4 A 142 THR ASN ASN ASP VAL ILE PHE THR GLY ALA ASN VAL GLU SEQRES 5 A 142 ASN ALA SER TYR SER ASN CYS ILE CYS ALA GLU ARG SER SEQRES 6 A 142 ALA MET ILE GLN VAL LEU MET ALA GLY HIS ARG SER GLY SEQRES 7 A 142 TRP LYS CYS MET VAL ILE CYS GLY ASP SER GLU ASP GLN SEQRES 8 A 142 CYS VAL SER PRO CYS GLY VAL CYS ARG GLN PHE ILE ASN SEQRES 9 A 142 GLU PHE VAL VAL LYS ASP PHE PRO ILE VAL MET LEU ASN SEQRES 10 A 142 SER THR GLY SER ARG SER LYS VAL MET THR MET GLY GLU SEQRES 11 A 142 LEU LEU PRO MET ALA PHE GLY PRO SER HIS LEU ASN SEQRES 1 B 142 MET LYS VAL GLY GLY ILE GLU ASP ARG GLN LEU GLU ALA SEQRES 2 B 142 LEU LYS ARG ALA ALA LEU LYS ALA CYS GLU LEU SER TYR SEQRES 3 B 142 SER PRO TYR SER HIS PHE ARG VAL GLY CYS SER ILE LEU SEQRES 4 B 142 THR ASN ASN ASP VAL ILE PHE THR GLY ALA ASN VAL GLU SEQRES 5 B 142 ASN ALA SER TYR SER ASN CYS ILE CYS ALA GLU ARG SER SEQRES 6 B 142 ALA MET ILE GLN VAL LEU MET ALA GLY HIS ARG SER GLY SEQRES 7 B 142 TRP LYS CYS MET VAL ILE CYS GLY ASP SER GLU ASP GLN SEQRES 8 B 142 CYS VAL SER PRO CYS GLY VAL CYS ARG GLN PHE ILE ASN SEQRES 9 B 142 GLU PHE VAL VAL LYS ASP PHE PRO ILE VAL MET LEU ASN SEQRES 10 B 142 SER THR GLY SER ARG SER LYS VAL MET THR MET GLY GLU SEQRES 11 B 142 LEU LEU PRO MET ALA PHE GLY PRO SER HIS LEU ASN SEQRES 1 C 142 MET LYS VAL GLY GLY ILE GLU ASP ARG GLN LEU GLU ALA SEQRES 2 C 142 LEU LYS ARG ALA ALA LEU LYS ALA CYS GLU LEU SER TYR SEQRES 3 C 142 SER PRO TYR SER HIS PHE ARG VAL GLY CYS SER ILE LEU SEQRES 4 C 142 THR ASN ASN ASP VAL ILE PHE THR GLY ALA ASN VAL GLU SEQRES 5 C 142 ASN ALA SER TYR SER ASN CYS ILE CYS ALA GLU ARG SER SEQRES 6 C 142 ALA MET ILE GLN VAL LEU MET ALA GLY HIS ARG SER GLY SEQRES 7 C 142 TRP LYS CYS MET VAL ILE CYS GLY ASP SER GLU ASP GLN SEQRES 8 C 142 CYS VAL SER PRO CYS GLY VAL CYS ARG GLN PHE ILE ASN SEQRES 9 C 142 GLU PHE VAL VAL LYS ASP PHE PRO ILE VAL MET LEU ASN SEQRES 10 C 142 SER THR GLY SER ARG SER LYS VAL MET THR MET GLY GLU SEQRES 11 C 142 LEU LEU PRO MET ALA PHE GLY PRO SER HIS LEU ASN SEQRES 1 D 142 MET LYS VAL GLY GLY ILE GLU ASP ARG GLN LEU GLU ALA SEQRES 2 D 142 LEU LYS ARG ALA ALA LEU LYS ALA CYS GLU LEU SER TYR SEQRES 3 D 142 SER PRO TYR SER HIS PHE ARG VAL GLY CYS SER ILE LEU SEQRES 4 D 142 THR ASN ASN ASP VAL ILE PHE THR GLY ALA ASN VAL GLU SEQRES 5 D 142 ASN ALA SER TYR SER ASN CYS ILE CYS ALA GLU ARG SER SEQRES 6 D 142 ALA MET ILE GLN VAL LEU MET ALA GLY HIS ARG SER GLY SEQRES 7 D 142 TRP LYS CYS MET VAL ILE CYS GLY ASP SER GLU ASP GLN SEQRES 8 D 142 CYS VAL SER PRO CYS GLY VAL CYS ARG GLN PHE ILE ASN SEQRES 9 D 142 GLU PHE VAL VAL LYS ASP PHE PRO ILE VAL MET LEU ASN SEQRES 10 D 142 SER THR GLY SER ARG SER LYS VAL MET THR MET GLY GLU SEQRES 11 D 142 LEU LEU PRO MET ALA PHE GLY PRO SER HIS LEU ASN
HET ZN A 150 1 HET ZN B 151 1 HET ZN C 152 1 HET ZN D 153 1
HETNAM ZN ZINC ION
FORMUL 5 ZN 4(ZN 2+) FORMUL 9 HOH *318(H2 O)
HELIX 1 1 GLU A 7 CYS A 22 1 16 HELIX 2 2 GLU A 23 SER A 25 5 3 HELIX 3 3 SER A 55 CYS A 59 5 5 HELIX 4 4 CYS A 61 ALA A 73 1 13 HELIX 5 5 CYS A 96 GLU A 105 1 10 HELIX 6 6 MET A 128 LEU A 132 1 5 HELIX 7 7 GLY A 137 LEU A 141 5 5 HELIX 8 8 GLU B 7 CYS B 22 1 16 HELIX 9 9 GLU B 23 SER B 25 5 3 HELIX 10 10 SER B 55 CYS B 59 5 5 HELIX 11 11 CYS B 61 ALA B 73 1 13 HELIX 12 12 CYS B 96 ASN B 104 1 9 HELIX 13 13 MET B 128 LEU B 132 1 5 HELIX 14 14 GLU C 7 CYS C 22 1 16 HELIX 15 15 GLU C 23 SER C 25 5 3 HELIX 16 16 SER C 55 CYS C 59 5 5 HELIX 17 17 CYS C 61 ALA C 73 1 13 HELIX 18 18 CYS C 96 GLU C 105 1 10 HELIX 19 19 MET C 128 LEU C 132 1 5 HELIX 20 20 GLY C 137 LEU C 141 5 5 HELIX 21 21 GLU D 7 CYS D 22 1 16 HELIX 22 22 GLU D 23 SER D 25 5 3 HELIX 23 23 SER D 55 CYS D 59 5 5 HELIX 24 24 CYS D 61 ALA D 73 1 13 HELIX 25 25 CYS D 96 GLU D 105 1 10 HELIX 26 26 MET D 128 LEU D 132 1 5
SHEET 1 A 5 ILE A 45 ALA A 49 0 SHEET 2 A 5 VAL A 34 LEU A 39 -1 N ILE A 38 O PHE A 46 SHEET 3 A 5 CYS A 81 GLY A 86 -1 O CYS A 85 N GLY A 35 SHEET 4 A 5 PRO A 112 LEU A 116 1 O VAL A 114 N MET A 82 SHEET 5 A 5 SER A 123 THR A 127 -1 O LYS A 124 N MET A 115 SHEET 1 B 5 ILE B 45 ALA B 49 0 SHEET 2 B 5 VAL B 34 LEU B 39 -1 N ILE B 38 O PHE B 46 SHEET 3 B 5 CYS B 81 GLY B 86 -1 O CYS B 85 N GLY B 35 SHEET 4 B 5 PRO B 112 LEU B 116 1 O VAL B 114 N MET B 82 SHEET 5 B 5 SER B 123 THR B 127 -1 O MET B 126 N ILE B 113 SHEET 1 C 5 ILE C 45 ALA C 49 0 SHEET 2 C 5 VAL C 34 LEU C 39 -1 N ILE C 38 O PHE C 46 SHEET 3 C 5 CYS C 81 GLY C 86 -1 O CYS C 85 N GLY C 35 SHEET 4 C 5 PRO C 112 LEU C 116 1 O VAL C 114 N MET C 82 SHEET 5 C 5 SER C 123 THR C 127 -1 O MET C 126 N ILE C 113 SHEET 1 D 5 ILE D 45 ALA D 49 0 SHEET 2 D 5 GLY D 35 LEU D 39 -1 N CYS D 36 O GLY D 48 SHEET 3 D 5 CYS D 81 CYS D 85 -1 O CYS D 85 N GLY D 35 SHEET 4 D 5 PRO D 112 LEU D 116 1 O VAL D 114 N MET D 82 SHEET 5 D 5 SER D 123 THR D 127 -1 O LYS D 124 N MET D 115
LINK ZN ZN A 150 SG CYS A 61 1555 1555 2.38 LINK ZN ZN A 150 SG CYS A 96 1555 1555 2.21 LINK ZN ZN A 150 SG CYS A 99 1555 1555 2.21 LINK ZN ZN B 151 SG CYS B 61 1555 1555 2.32 LINK ZN ZN B 151 SG CYS B 96 1555 1555 2.35 LINK ZN ZN B 151 SG CYS B 99 1555 1555 2.23 LINK ZN ZN C 152 SG CYS C 61 1555 1555 2.35 LINK ZN ZN C 152 SG CYS C 96 1555 1555 2.27 LINK ZN ZN C 152 SG CYS C 99 1555 1555 2.33 LINK ZN ZN D 153 SG CYS D 61 1555 1555 2.40 LINK ZN ZN D 153 SG CYS D 96 1555 1555 2.36 LINK ZN ZN D 153 SG CYS D 99 1555 1555 2.33 LINK ZN ZN A 150 O HOH A 223 1555 1555 2.11 LINK ZN ZN B 151 O HOH B 209 1555 1555 2.22 LINK ZN ZN C 152 O HOH C 198 1555 1555 2.15 LINK ZN ZN D 153 O HOH D 179 1555 1555 2.03
SITE 1 AC1 4 CYS A 61 CYS A 96 CYS A 99 HOH A 223 SITE 1 AC2 4 CYS B 61 CYS B 96 CYS B 99 HOH B 209 SITE 1 AC3 4 CYS C 61 CYS C 96 CYS C 99 HOH C 198 SITE 1 AC4 4 CYS D 61 CYS D 96 CYS D 99 HOH D 179
CRYST1 78.520 86.370 156.260 90.00 90.00 90.00 C 2 2 21 32
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 0.012736 0.000000 0.000000 0.00000
SCALE2 0.000000 0.011578 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006400 0.00000