HEADER HYDROLASE 19-APR-16 5JFY TITLE CRYSTAL STRUCTURE OF A PLANT CYTIDINE DEAMINASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYCYTIDINE DEAMINASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: UNP RESIDUES 19-153; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRASSICA OLERACEA VAR. CAPITATA; SOURCE 3 ORGANISM_COMMON: CABBAGE; SOURCE 4 ORGANISM_TAXID: 3716; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET46 EK/LIC KEYWDS CYTIDINE DEAMINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.W.TAYLOR,J.E.LEE REVDAT 5 27-SEP-23 5JFY 1 LINK REVDAT 4 08-JAN-20 5JFY 1 REMARK REVDAT 3 27-SEP-17 5JFY 1 REMARK REVDAT 2 03-MAY-17 5JFY 1 REMARK REVDAT 1 26-APR-17 5JFY 0 JRNL AUTH M.W.TAYLOR,J.E.LEE JRNL TITL TO BE PUBLISHED JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 37797 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.670 REMARK 3 FREE R VALUE TEST SET COUNT : 1952 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 44.6456 - 5.0602 0.88 2789 136 0.1953 0.2353 REMARK 3 2 5.0602 - 4.0173 0.96 2863 142 0.1437 0.1844 REMARK 3 3 4.0173 - 3.5097 0.98 2888 141 0.1423 0.1718 REMARK 3 4 3.5097 - 3.1889 0.99 2870 142 0.1499 0.1554 REMARK 3 5 3.1889 - 2.9604 0.99 2896 142 0.1640 0.2204 REMARK 3 6 2.9604 - 2.7859 0.99 2882 143 0.1676 0.1900 REMARK 3 7 2.7859 - 2.6464 1.00 2878 139 0.1869 0.2057 REMARK 3 8 2.6464 - 2.5312 1.00 2874 139 0.1983 0.2445 REMARK 3 9 2.5312 - 2.4338 0.99 2851 140 0.2078 0.2671 REMARK 3 10 2.4338 - 2.3498 0.99 2882 140 0.2208 0.2419 REMARK 3 11 2.3498 - 2.2763 0.99 2833 139 0.2368 0.2616 REMARK 3 12 2.2763 - 2.2112 0.99 2822 139 0.2526 0.2895 REMARK 3 13 2.2112 - 2.1530 0.99 2866 140 0.2721 0.3046 REMARK 3 14 2.1530 - 2.1005 0.93 2672 130 0.2964 0.3196 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.21 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 : 0.003 3659 REMARK 3 ANGLE : 0.500 4943 REMARK 3 CHIRALITY : 0.043 558 REMARK 3 PLANARITY : 0.003 645 REMARK 3 DIHEDRAL : 17.607 1290 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 5JFY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000220315. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97949 REMARK 200 MONOCHROMATOR : ACCEL/BRUKER DOUBLE CRYSTAL REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR: ULTRA REMARK 200 -LOW EXPANSION (ULE) TITANIUM REMARK 200 SILIICATE FLAT MIRROR WITH PT, REMARK 200 UNCOATED, AND PD STRIPS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41687 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 47.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.16 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.00 REMARK 200 R MERGE FOR SHELL (I) : 0.60700 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 2.6.0 REMARK 200 STARTING MODEL: 2B3J REMARK 200 REMARK 200 REMARK: BIPYRAMIDAL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.93 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.0085 M COCL2, 0.085 SODIUM ACETATE REMARK 280 PH 4.6, 0.85 M 1,6-HEXANEDIOL, 15% (V/V) GLYCEROL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 71.53050 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 49.90400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 49.90400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 107.29575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 49.90400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 49.90400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.76525 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 49.90400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.90400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 107.29575 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 49.90400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.90400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.76525 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 71.53050 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: 2550 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 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: 2830 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -112.0 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 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 C ACT B 204 LIES ON A SPECIAL POSITION. REMARK 375 CH3 ACT B 204 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 GLY A 15 REMARK 465 SER A 16 REMARK 465 SER A 17 REMARK 465 GLY A 18 REMARK 465 PHE A 19 REMARK 465 ALA A 20 REMARK 465 ASP A 140 REMARK 465 ASP A 141 REMARK 465 PHE A 142 REMARK 465 ILE A 143 REMARK 465 ALA A 144 REMARK 465 ASP A 145 REMARK 465 ALA A 146 REMARK 465 LEU A 147 REMARK 465 ARG A 148 REMARK 465 GLY A 149 REMARK 465 THR A 150 REMARK 465 GLY A 151 REMARK 465 VAL A 152 REMARK 465 TYR A 153 REMARK 465 GLY B 15 REMARK 465 SER B 16 REMARK 465 SER B 17 REMARK 465 GLY B 18 REMARK 465 PHE B 19 REMARK 465 ALA B 20 REMARK 465 ASP B 140 REMARK 465 ASP B 141 REMARK 465 PHE B 142 REMARK 465 ILE B 143 REMARK 465 ALA B 144 REMARK 465 ASP B 145 REMARK 465 ALA B 146 REMARK 465 LEU B 147 REMARK 465 ARG B 148 REMARK 465 GLY B 149 REMARK 465 THR B 150 REMARK 465 GLY B 151 REMARK 465 VAL B 152 REMARK 465 TYR B 153 REMARK 465 GLY C 15 REMARK 465 SER C 16 REMARK 465 SER C 17 REMARK 465 GLY C 18 REMARK 465 PHE C 19 REMARK 465 ASP C 141 REMARK 465 PHE C 142 REMARK 465 ILE C 143 REMARK 465 ALA C 144 REMARK 465 ASP C 145 REMARK 465 ALA C 146 REMARK 465 LEU C 147 REMARK 465 ARG C 148 REMARK 465 GLY C 149 REMARK 465 THR C 150 REMARK 465 GLY C 151 REMARK 465 VAL C 152 REMARK 465 TYR C 153 REMARK 465 GLY D 15 REMARK 465 SER D 16 REMARK 465 SER D 17 REMARK 465 GLY D 18 REMARK 465 PHE D 19 REMARK 465 ALA D 20 REMARK 465 LYS D 130 REMARK 465 ALA D 131 REMARK 465 ASP D 140 REMARK 465 ASP D 141 REMARK 465 PHE D 142 REMARK 465 ILE D 143 REMARK 465 ALA D 144 REMARK 465 ASP D 145 REMARK 465 ALA D 146 REMARK 465 LEU D 147 REMARK 465 ARG D 148 REMARK 465 GLY D 149 REMARK 465 THR D 150 REMARK 465 GLY D 151 REMARK 465 VAL D 152 REMARK 465 TYR D 153 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 B 60 CG CD CE NZ REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 LYS B 91 CE NZ REMARK 470 LYS B 123 CE NZ REMARK 470 LYS C 43 NZ REMARK 470 LYS C 60 CG CD CE NZ REMARK 470 GLU C 62 CG CD OE1 OE2 REMARK 470 LYS C 91 CE NZ REMARK 470 LYS C 92 CE NZ REMARK 470 ASP C 140 CG OD1 OD2 REMARK 470 ASP D 28 CG OD1 OD2 REMARK 470 GLU D 39 CG CD OE1 OE2 REMARK 470 LYS D 60 CG CD CE NZ REMARK 470 ASN D 61 CG OD1 ND2 REMARK 470 GLU D 62 CG CD OE1 OE2 REMARK 470 LYS D 92 CG CD CE NZ REMARK 470 LYS D 123 CG CD CE NZ 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 OE1 GLU B 88 O HOH B 301 2.09 REMARK 500 O HOH B 320 O HOH B 353 2.13 REMARK 500 OE1 GLU A 97 O HOH A 301 2.15 REMARK 500 O HOH A 336 O HOH A 356 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 364 O HOH C 325 4445 2.12 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 79 48.72 -81.95 REMARK 500 ALA A 133 -43.09 66.68 REMARK 500 ALA B 133 -49.80 71.52 REMARK 500 ALA C 79 46.60 -83.63 REMARK 500 ALA C 133 -52.86 72.07 REMARK 500 ASN D 61 -1.98 69.85 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 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 80 ND1 REMARK 620 2 CYS A 110 SG 105.0 REMARK 620 3 CYS A 113 SG 115.6 113.9 REMARK 620 4 HOH C 321 O 108.2 114.3 100.1 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 HOH A 332 O REMARK 620 2 HIS C 80 ND1 115.6 REMARK 620 3 CYS C 110 SG 111.0 100.0 REMARK 620 4 CYS C 113 SG 102.4 114.9 113.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 80 ND1 REMARK 620 2 CYS B 110 SG 106.9 REMARK 620 3 CYS B 113 SG 115.3 115.7 REMARK 620 4 HOH B 333 O 106.7 113.7 98.2 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 80 ND1 REMARK 620 2 CYS D 110 SG 109.2 REMARK 620 3 CYS D 113 SG 107.8 116.7 REMARK 620 4 HOH D 316 O 114.9 105.4 103.0 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 CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEZ A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT C 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL D 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN D 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEZ D 203 DBREF 5JFY A 19 153 UNP H2EMX8 H2EMX8_BRAOC 19 153 DBREF 5JFY B 19 153 UNP H2EMX8 H2EMX8_BRAOC 19 153 DBREF 5JFY C 19 153 UNP H2EMX8 H2EMX8_BRAOC 19 153 DBREF 5JFY D 19 153 UNP H2EMX8 H2EMX8_BRAOC 19 153 SEQADV 5JFY GLY A 15 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER A 16 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER A 17 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY GLY A 18 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY GLY B 15 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER B 16 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER B 17 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY GLY B 18 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY GLY C 15 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER C 16 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER C 17 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY GLY C 18 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY GLY D 15 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER D 16 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY SER D 17 UNP H2EMX8 EXPRESSION TAG SEQADV 5JFY GLY D 18 UNP H2EMX8 EXPRESSION TAG SEQRES 1 A 139 GLY SER SER GLY PHE ALA GLY HIS GLN GLN ALA VAL LEU SEQRES 2 A 139 ASP SER ASP HIS LYS PHE LEU THR GLN ALA VAL GLU GLU SEQRES 3 A 139 ALA TYR LYS GLY VAL ASP CYS GLY ASP GLY GLY PRO PHE SEQRES 4 A 139 GLY ALA VAL ILE VAL HIS LYS ASN GLU VAL VAL ALA SER SEQRES 5 A 139 CYS HIS ASN MET VAL LEU LYS TYR THR ASP PRO THR ALA SEQRES 6 A 139 HIS ALA GLU VAL THR ALA ILE ARG GLU ALA CYS LYS LYS SEQRES 7 A 139 LEU ASN GLN ILE GLU LEU SER GLU CYS GLU ILE TYR ALA SEQRES 8 A 139 SER CYS GLU PRO CYS PRO MET CYS PHE GLY ALA ILE HIS SEQRES 9 A 139 LEU SER ARG LEU LYS ARG LEU VAL TYR GLY ALA LYS ALA SEQRES 10 A 139 GLU ALA ALA ILE ALA ILE GLY PHE ASP ASP PHE ILE ALA SEQRES 11 A 139 ASP ALA LEU ARG GLY THR GLY VAL TYR SEQRES 1 B 139 GLY SER SER GLY PHE ALA GLY HIS GLN GLN ALA VAL LEU SEQRES 2 B 139 ASP SER ASP HIS LYS PHE LEU THR GLN ALA VAL GLU GLU SEQRES 3 B 139 ALA TYR LYS GLY VAL ASP CYS GLY ASP GLY GLY PRO PHE SEQRES 4 B 139 GLY ALA VAL ILE VAL HIS LYS ASN GLU VAL VAL ALA SER SEQRES 5 B 139 CYS HIS ASN MET VAL LEU LYS TYR THR ASP PRO THR ALA SEQRES 6 B 139 HIS ALA GLU VAL THR ALA ILE ARG GLU ALA CYS LYS LYS SEQRES 7 B 139 LEU ASN GLN ILE GLU LEU SER GLU CYS GLU ILE TYR ALA SEQRES 8 B 139 SER CYS GLU PRO CYS PRO MET CYS PHE GLY ALA ILE HIS SEQRES 9 B 139 LEU SER ARG LEU LYS ARG LEU VAL TYR GLY ALA LYS ALA SEQRES 10 B 139 GLU ALA ALA ILE ALA ILE GLY PHE ASP ASP PHE ILE ALA SEQRES 11 B 139 ASP ALA LEU ARG GLY THR GLY VAL TYR SEQRES 1 C 139 GLY SER SER GLY PHE ALA GLY HIS GLN GLN ALA VAL LEU SEQRES 2 C 139 ASP SER ASP HIS LYS PHE LEU THR GLN ALA VAL GLU GLU SEQRES 3 C 139 ALA TYR LYS GLY VAL ASP CYS GLY ASP GLY GLY PRO PHE SEQRES 4 C 139 GLY ALA VAL ILE VAL HIS LYS ASN GLU VAL VAL ALA SER SEQRES 5 C 139 CYS HIS ASN MET VAL LEU LYS TYR THR ASP PRO THR ALA SEQRES 6 C 139 HIS ALA GLU VAL THR ALA ILE ARG GLU ALA CYS LYS LYS SEQRES 7 C 139 LEU ASN GLN ILE GLU LEU SER GLU CYS GLU ILE TYR ALA SEQRES 8 C 139 SER CYS GLU PRO CYS PRO MET CYS PHE GLY ALA ILE HIS SEQRES 9 C 139 LEU SER ARG LEU LYS ARG LEU VAL TYR GLY ALA LYS ALA SEQRES 10 C 139 GLU ALA ALA ILE ALA ILE GLY PHE ASP ASP PHE ILE ALA SEQRES 11 C 139 ASP ALA LEU ARG GLY THR GLY VAL TYR SEQRES 1 D 139 GLY SER SER GLY PHE ALA GLY HIS GLN GLN ALA VAL LEU SEQRES 2 D 139 ASP SER ASP HIS LYS PHE LEU THR GLN ALA VAL GLU GLU SEQRES 3 D 139 ALA TYR LYS GLY VAL ASP CYS GLY ASP GLY GLY PRO PHE SEQRES 4 D 139 GLY ALA VAL ILE VAL HIS LYS ASN GLU VAL VAL ALA SER SEQRES 5 D 139 CYS HIS ASN MET VAL LEU LYS TYR THR ASP PRO THR ALA SEQRES 6 D 139 HIS ALA GLU VAL THR ALA ILE ARG GLU ALA CYS LYS LYS SEQRES 7 D 139 LEU ASN GLN ILE GLU LEU SER GLU CYS GLU ILE TYR ALA SEQRES 8 D 139 SER CYS GLU PRO CYS PRO MET CYS PHE GLY ALA ILE HIS SEQRES 9 D 139 LEU SER ARG LEU LYS ARG LEU VAL TYR GLY ALA LYS ALA SEQRES 10 D 139 GLU ALA ALA ILE ALA ILE GLY PHE ASP ASP PHE ILE ALA SEQRES 11 D 139 ASP ALA LEU ARG GLY THR GLY VAL TYR HET CL A 201 1 HET ZN A 202 1 HET ACT A 203 7 HET HEZ A 204 22 HET CL B 201 1 HET ZN B 202 1 HET ACT B 203 7 HET ACT B 204 7 HET CL C 201 1 HET ZN C 202 1 HET GOL C 203 14 HET GOL C 204 14 HET GOL C 205 14 HET ACT C 206 7 HET CL D 201 1 HET ZN D 202 1 HET HEZ D 203 22 HETNAM CL CHLORIDE ION HETNAM ZN ZINC ION HETNAM ACT ACETATE ION HETNAM HEZ HEXANE-1,6-DIOL HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 CL 4(CL 1-) FORMUL 6 ZN 4(ZN 2+) FORMUL 7 ACT 4(C2 H3 O2 1-) FORMUL 8 HEZ 2(C6 H14 O2) FORMUL 15 GOL 3(C3 H8 O3) FORMUL 22 HOH *199(H2 O) HELIX 1 AA1 LEU A 27 SER A 29 5 3 HELIX 2 AA2 ASP A 30 GLY A 48 1 19 HELIX 3 AA3 MET A 70 THR A 75 1 6 HELIX 4 AA4 HIS A 80 ASN A 94 1 15 HELIX 5 AA5 CYS A 110 ARG A 121 1 12 HELIX 6 AA6 SER B 29 CYS B 47 1 19 HELIX 7 AA7 MET B 70 THR B 75 1 6 HELIX 8 AA8 HIS B 80 ASN B 94 1 15 HELIX 9 AA9 CYS B 110 SER B 120 1 11 HELIX 10 AB1 LEU C 27 SER C 29 5 3 HELIX 11 AB2 ASP C 30 CYS C 47 1 18 HELIX 12 AB3 MET C 70 THR C 75 1 6 HELIX 13 AB4 HIS C 80 ASN C 94 1 15 HELIX 14 AB5 CYS C 110 ARG C 121 1 12 HELIX 15 AB6 LEU D 27 SER D 29 5 3 HELIX 16 AB7 ASP D 30 CYS D 47 1 18 HELIX 17 AB8 MET D 70 THR D 75 1 6 HELIX 18 AB9 HIS D 80 ASN D 94 1 15 HELIX 19 AC1 CYS D 110 SER D 120 1 11 SHEET 1 AA1 6 HIS A 22 GLN A 24 0 SHEET 2 AA1 6 ALA A 134 GLY A 138 -1 O GLY A 138 N HIS A 22 SHEET 3 AA1 6 ARG A 124 GLY A 128 -1 N LEU A 125 O ILE A 137 SHEET 4 AA1 6 CYS A 101 ALA A 105 1 N ALA A 105 O VAL A 126 SHEET 5 AA1 6 GLY A 54 HIS A 59 -1 N VAL A 56 O TYR A 104 SHEET 6 AA1 6 GLU A 62 HIS A 68 -1 O GLU A 62 N HIS A 59 SHEET 1 AA2 6 HIS B 22 GLN B 24 0 SHEET 2 AA2 6 ALA B 133 GLY B 138 -1 O ALA B 136 N GLN B 24 SHEET 3 AA2 6 ARG B 124 ALA B 129 -1 N LEU B 125 O ILE B 137 SHEET 4 AA2 6 GLU B 102 ALA B 105 1 N ALA B 105 O VAL B 126 SHEET 5 AA2 6 GLY B 54 HIS B 59 -1 N VAL B 56 O TYR B 104 SHEET 6 AA2 6 GLU B 62 HIS B 68 -1 O GLU B 62 N HIS B 59 SHEET 1 AA3 6 HIS C 22 GLN C 24 0 SHEET 2 AA3 6 ALA C 133 GLY C 138 -1 O GLY C 138 N HIS C 22 SHEET 3 AA3 6 ARG C 124 ALA C 129 -1 N LEU C 125 O ILE C 137 SHEET 4 AA3 6 GLU C 102 ALA C 105 1 N ALA C 105 O VAL C 126 SHEET 5 AA3 6 GLY C 54 HIS C 59 -1 N VAL C 56 O TYR C 104 SHEET 6 AA3 6 GLU C 62 HIS C 68 -1 O GLU C 62 N HIS C 59 SHEET 1 AA4 6 HIS D 22 GLN D 24 0 SHEET 2 AA4 6 ILE D 135 GLY D 138 -1 O GLY D 138 N HIS D 22 SHEET 3 AA4 6 ARG D 124 TYR D 127 -1 N LEU D 125 O ILE D 137 SHEET 4 AA4 6 GLU D 102 ALA D 105 1 N ILE D 103 O ARG D 124 SHEET 5 AA4 6 GLY D 54 HIS D 59 -1 N VAL D 56 O TYR D 104 SHEET 6 AA4 6 GLU D 62 HIS D 68 -1 O VAL D 64 N ILE D 57 LINK ND1 HIS A 80 ZN ZN A 202 1555 1555 2.09 LINK SG CYS A 110 ZN ZN A 202 1555 1555 2.33 LINK SG CYS A 113 ZN ZN A 202 1555 1555 2.31 LINK ZN ZN A 202 O HOH C 321 1555 1555 2.10 LINK O HOH A 332 ZN ZN C 202 1555 1555 2.30 LINK ND1 HIS B 80 ZN ZN B 202 1555 1555 2.05 LINK SG CYS B 110 ZN ZN B 202 1555 1555 2.28 LINK SG CYS B 113 ZN ZN B 202 1555 1555 2.32 LINK ZN ZN B 202 O HOH B 333 1555 1555 2.07 LINK ND1 HIS C 80 ZN ZN C 202 1555 1555 2.07 LINK SG CYS C 110 ZN ZN C 202 1555 1555 2.29 LINK SG CYS C 113 ZN ZN C 202 1555 1555 2.30 LINK ND1 HIS D 80 ZN ZN D 202 1555 1555 1.95 LINK SG CYS D 110 ZN ZN D 202 1555 1555 2.37 LINK SG CYS D 113 ZN ZN D 202 1555 1555 2.26 LINK ZN ZN D 202 O HOH D 316 1555 1555 2.26 SITE 1 AC1 5 PHE A 53 ASN A 69 HIS A 80 ALA A 81 SITE 2 AC1 5 LYS C 130 SITE 1 AC2 4 HIS A 80 CYS A 110 CYS A 113 HOH C 321 SITE 1 AC3 3 GLU A 108 GLY A 128 LYS A 130 SITE 1 AC4 2 GLY A 21 GLN A 23 SITE 1 AC5 5 PHE B 53 ASN B 69 HIS B 80 ALA B 81 SITE 2 AC5 5 LYS B 130 SITE 1 AC6 4 HIS B 80 CYS B 110 CYS B 113 HOH B 333 SITE 1 AC7 5 PHE B 53 GLU B 108 GLY B 128 ALA B 129 SITE 2 AC7 5 LYS B 130 SITE 1 AC8 3 PRO B 52 PHE B 53 SER B 106 SITE 1 AC9 5 LYS A 130 PHE C 53 ASN C 69 HIS C 80 SITE 2 AC9 5 ALA C 81 SITE 1 AD1 4 HOH A 332 HIS C 80 CYS C 110 CYS C 113 SITE 1 AD2 8 ALA A 41 PRO A 52 PHE A 53 SER A 106 SITE 2 AD2 8 PRO C 52 PHE C 53 SER C 106 CYS C 107 SITE 1 AD3 8 VAL A 63 VAL A 64 ALA A 65 LYS A 92 SITE 2 AD3 8 HOH A 302 LEU C 27 ASP C 28 SER C 29 SITE 1 AD4 5 GLU C 108 GLY C 128 ALA C 129 LYS C 130 SITE 2 AD4 5 HOH C 322 SITE 1 AD5 2 GLY C 48 LYS C 73 SITE 1 AD6 7 PHE D 53 ASN D 69 HIS D 80 ALA D 81 SITE 2 AD6 7 GLU D 82 HOH D 308 HOH D 326 SITE 1 AD7 4 HIS D 80 CYS D 110 CYS D 113 HOH D 316 SITE 1 AD8 3 GLY D 51 ASN D 69 HOH D 317 CRYST1 99.808 99.808 143.061 90.00 90.00 90.00 P 43 21 2 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 0.010019 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010019 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006990 0.00000