HEADER HYDROLASE 06-SEP-19 6KW6 TITLE CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM STREPTOMYCES NOURSEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDINE DEAMINASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES NOURSEI; SOURCE 3 ORGANISM_TAXID: 1971; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.XIE,Z.C.LIU,G.G.WANG REVDAT 2 22-NOV-23 6KW6 1 REMARK REVDAT 1 09-SEP-20 6KW6 0 JRNL AUTH T.XIE,Z.C.LIU,G.G.WANG JRNL TITL CRYSTAL STRUCTURE OF CYTIDINE DEAMINASE FROM STREPTOMYCES JRNL TITL 2 NOURSEI JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 19486 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.700 REMARK 3 FREE R VALUE TEST SET COUNT : 916 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.9330 - 3.6241 0.97 2653 153 0.1618 0.1836 REMARK 3 2 3.6241 - 2.8773 0.99 2703 141 0.1660 0.1808 REMARK 3 3 2.8773 - 2.5138 0.99 2654 130 0.1800 0.1937 REMARK 3 4 2.5138 - 2.2840 0.98 2692 114 0.1660 0.1924 REMARK 3 5 2.2840 - 2.1204 0.98 2656 132 0.1660 0.2234 REMARK 3 6 2.1204 - 1.9954 0.98 2661 119 0.1680 0.2097 REMARK 3 7 1.9954 - 1.8955 0.94 2551 127 0.2011 0.2484 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1740 REMARK 3 ANGLE : 0.824 2370 REMARK 3 CHIRALITY : 0.054 270 REMARK 3 PLANARITY : 0.005 316 REMARK 3 DIHEDRAL : 14.255 1026 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6KW6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013746. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAY-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97916 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19489 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.890 REMARK 200 RESOLUTION RANGE LOW (A) : 29.933 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.47600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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: 3MPZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1M TRIS PH8.5 AND 25% W/V POLYETHYLENE GLYCOL 3,350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 33.88650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.12950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 33.88650 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 37.12950 REMARK 290 SMTRY3 4 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: 7900 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -212.0 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 BIOMT1 2 -1.000000 0.000000 0.000000 52.71943 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 50.59295 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 A 313 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 313 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 -7 REMARK 465 THR A -6 REMARK 465 HIS A -5 REMARK 465 ASP A -4 REMARK 465 VAL A -3 REMARK 465 PRO A -2 REMARK 465 VAL A -1 REMARK 465 THR A 0 REMARK 465 PHE A 120 REMARK 465 GLY A 121 REMARK 465 PRO A 122 REMARK 465 GLY A 123 REMARK 465 HIS A 124 REMARK 465 LEU A 125 REMARK 465 THR A 126 REMARK 465 ARG A 127 REMARK 465 MET B -7 REMARK 465 THR B -6 REMARK 465 HIS B -5 REMARK 465 ASP B -4 REMARK 465 VAL B -3 REMARK 465 PRO B -2 REMARK 465 VAL B -1 REMARK 465 THR B 0 REMARK 465 PHE B 120 REMARK 465 GLY B 121 REMARK 465 PRO B 122 REMARK 465 GLY B 123 REMARK 465 HIS B 124 REMARK 465 LEU B 125 REMARK 465 THR B 126 REMARK 465 ARG B 127 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 A 355 O HOH A 362 1.87 REMARK 500 O HOH A 311 O HOH A 366 2.05 REMARK 500 OH TYR A 24 O HOH A 301 2.14 REMARK 500 OD1 ASP B 100 O HOH B 301 2.14 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 53 SG REMARK 620 2 CYS A 86 SG 119.9 REMARK 620 3 CYS A 89 SG 98.7 115.1 REMARK 620 N 1 2 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 53 SG REMARK 620 2 CYS B 86 SG 117.9 REMARK 620 3 CYS B 89 SG 100.5 118.4 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 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 DBREF 6KW6 A -7 127 PDB 6KW6 6KW6 -7 127 DBREF 6KW6 B -7 127 PDB 6KW6 6KW6 -7 127 SEQRES 1 A 135 MET THR HIS ASP VAL PRO VAL THR ILE ASP TRP PRO ALA SEQRES 2 A 135 LEU ARG THR GLN ALA ARG ASP ALA MET SER ARG ALA TYR SEQRES 3 A 135 ALA PRO TYR SER GLY TYR PRO VAL GLY ALA ALA ALA LEU SEQRES 4 A 135 VAL ASP ASP GLY ARG THR VAL THR GLY CYS ASN VAL GLU SEQRES 5 A 135 ASN ALA SER TYR GLY LEU GLY LEU CYS ALA GLU CYS GLY SEQRES 6 A 135 LEU VAL SER ALA LEU PHE ALA SER GLY GLY GLY ARG LEU SEQRES 7 A 135 THR ALA PHE THR CYS VAL ASP GLY LYS GLY GLU LEU LEU SEQRES 8 A 135 VAL PRO CYS GLY ARG CYS ARG GLN LEU LEU HIS GLU HIS SEQRES 9 A 135 GLY GLY PRO ASP LEU LEU VAL ASP THR ALA ALA GLY ILE SEQRES 10 A 135 ARG PRO LEU ALA ALA LEU LEU PRO ASP ALA PHE GLY PRO SEQRES 11 A 135 GLY HIS LEU THR ARG SEQRES 1 B 135 MET THR HIS ASP VAL PRO VAL THR ILE ASP TRP PRO ALA SEQRES 2 B 135 LEU ARG THR GLN ALA ARG ASP ALA MET SER ARG ALA TYR SEQRES 3 B 135 ALA PRO TYR SER GLY TYR PRO VAL GLY ALA ALA ALA LEU SEQRES 4 B 135 VAL ASP ASP GLY ARG THR VAL THR GLY CYS ASN VAL GLU SEQRES 5 B 135 ASN ALA SER TYR GLY LEU GLY LEU CYS ALA GLU CYS GLY SEQRES 6 B 135 LEU VAL SER ALA LEU PHE ALA SER GLY GLY GLY ARG LEU SEQRES 7 B 135 THR ALA PHE THR CYS VAL ASP GLY LYS GLY GLU LEU LEU SEQRES 8 B 135 VAL PRO CYS GLY ARG CYS ARG GLN LEU LEU HIS GLU HIS SEQRES 9 B 135 GLY GLY PRO ASP LEU LEU VAL ASP THR ALA ALA GLY ILE SEQRES 10 B 135 ARG PRO LEU ALA ALA LEU LEU PRO ASP ALA PHE GLY PRO SEQRES 11 B 135 GLY HIS LEU THR ARG HET ZN A 201 1 HET ZN B 201 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *154(H2 O) HELIX 1 AA1 ASP A 2 SER A 15 1 14 HELIX 2 AA2 SER A 47 GLY A 51 5 5 HELIX 3 AA3 CYS A 53 SER A 65 1 13 HELIX 4 AA4 CYS A 86 GLY A 98 1 13 HELIX 5 AA5 LEU A 112 LEU A 116 1 5 HELIX 6 AA6 ASP B 2 SER B 15 1 14 HELIX 7 AA7 SER B 47 GLY B 51 5 5 HELIX 8 AA8 CYS B 53 SER B 65 1 13 HELIX 9 AA9 CYS B 86 GLY B 98 1 13 HELIX 10 AB1 LEU B 112 LEU B 116 1 5 SHEET 1 AA1 5 THR A 37 CYS A 41 0 SHEET 2 AA1 5 VAL A 26 VAL A 32 -1 N ALA A 28 O GLY A 40 SHEET 3 AA1 5 LEU A 70 ASP A 77 -1 O THR A 71 N LEU A 31 SHEET 4 AA1 5 LEU A 102 THR A 105 1 O ASP A 104 N PHE A 73 SHEET 5 AA1 5 GLY A 108 PRO A 111 -1 O ARG A 110 N VAL A 103 SHEET 1 AA2 5 THR B 37 CYS B 41 0 SHEET 2 AA2 5 GLY B 27 VAL B 32 -1 N ALA B 28 O GLY B 40 SHEET 3 AA2 5 LEU B 70 VAL B 76 -1 O THR B 71 N LEU B 31 SHEET 4 AA2 5 LEU B 102 VAL B 103 1 O LEU B 102 N PHE B 73 SHEET 5 AA2 5 ARG B 110 PRO B 111 -1 O ARG B 110 N VAL B 103 LINK SG CYS A 53 ZN ZN A 201 1555 1555 2.42 LINK SG CYS A 86 ZN ZN A 201 1555 1555 2.41 LINK SG CYS A 89 ZN ZN A 201 1555 1555 2.28 LINK SG CYS B 53 ZN ZN B 201 1555 1555 2.42 LINK SG CYS B 86 ZN ZN B 201 1555 1555 2.39 LINK SG CYS B 89 ZN ZN B 201 1555 1555 2.23 SITE 1 AC1 4 CYS A 53 CYS A 86 CYS A 89 HOH A 315 SITE 1 AC2 4 CYS B 53 CYS B 86 CYS B 89 HOH B 341 CRYST1 67.773 74.259 52.785 90.00 106.57 90.00 C 1 2 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 0.014755 0.000000 0.004391 0.00000 SCALE2 0.000000 0.013466 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019766 0.00000