HEADER HYDROLASE/HYDROLASE INHIBITOR 31-JUL-10 3O7U TITLE CRYSTAL STRUCTURE OF CYTOSINE DEAMINASE FROM ESCHERICHIA COLI TITLE 2 COMPLEXED WITH ZINC AND PHOSPHONO-CYTOSINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSINE DEAMINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: CODA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS (BETA-ALPHA)8 BARREL, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.A.FEDOROV,E.V.FEDOROV,R.S.HALL,F.M.RAUSHEL,S.C.ALMO REVDAT 5 04-OCT-23 3O7U 1 LINK REVDAT 4 06-SEP-23 3O7U 1 REMARK LINK REVDAT 3 07-MAR-12 3O7U 1 HEADER KEYWDS REVDAT 2 16-NOV-11 3O7U 1 VERSN HETATM REVDAT 1 15-JUN-11 3O7U 0 JRNL AUTH R.S.HALL,A.A.FEDOROV,C.XU,E.V.FEDOROV,S.C.ALMO,F.M.RAUSHEL JRNL TITL THREE-DIMENSIONAL STRUCTURE AND CATALYTIC MECHANISM OF JRNL TITL 2 CYTOSINE DEAMINASE. JRNL REF BIOCHEMISTRY V. 50 5077 2011 JRNL REFN ISSN 0006-2960 JRNL PMID 21545144 JRNL DOI 10.1021/BI200483K REMARK 2 REMARK 2 RESOLUTION. 1.71 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.71 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 86951 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 4360 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 39.2184 - 5.3019 1.00 2932 161 0.1706 0.1739 REMARK 3 2 5.3019 - 4.2098 1.00 2840 151 0.1380 0.1525 REMARK 3 3 4.2098 - 3.6781 1.00 2812 160 0.1388 0.1489 REMARK 3 4 3.6781 - 3.3420 1.00 2802 141 0.1382 0.1525 REMARK 3 5 3.3420 - 3.1026 1.00 2829 137 0.1480 0.1788 REMARK 3 6 3.1026 - 2.9197 1.00 2787 146 0.1570 0.1828 REMARK 3 7 2.9197 - 2.7736 1.00 2795 153 0.1617 0.1968 REMARK 3 8 2.7736 - 2.6529 1.00 2820 125 0.1618 0.2043 REMARK 3 9 2.6529 - 2.5508 1.00 2766 141 0.1563 0.1727 REMARK 3 10 2.5508 - 2.4627 1.00 2763 161 0.1580 0.2029 REMARK 3 11 2.4627 - 2.3858 1.00 2772 157 0.1603 0.1934 REMARK 3 12 2.3858 - 2.3176 1.00 2783 139 0.1609 0.1793 REMARK 3 13 2.3176 - 2.2566 1.00 2773 159 0.1619 0.1901 REMARK 3 14 2.2566 - 2.2015 1.00 2766 140 0.1659 0.1824 REMARK 3 15 2.2015 - 2.1515 1.00 2794 140 0.1716 0.1835 REMARK 3 16 2.1515 - 2.1057 1.00 2723 157 0.1757 0.2023 REMARK 3 17 2.1057 - 2.0636 1.00 2770 154 0.1772 0.2029 REMARK 3 18 2.0636 - 2.0246 1.00 2800 123 0.1744 0.1745 REMARK 3 19 2.0246 - 1.9885 1.00 2750 155 0.1933 0.2260 REMARK 3 20 1.9885 - 1.9548 1.00 2804 144 0.2028 0.2207 REMARK 3 21 1.9548 - 1.9232 1.00 2767 145 0.2068 0.1978 REMARK 3 22 1.9232 - 1.8936 1.00 2746 161 0.2205 0.2596 REMARK 3 23 1.8936 - 1.8658 1.00 2788 138 0.2380 0.2530 REMARK 3 24 1.8658 - 1.8395 1.00 2710 144 0.2472 0.3024 REMARK 3 25 1.8395 - 1.8147 1.00 2770 155 0.2459 0.2701 REMARK 3 26 1.8147 - 1.7911 1.00 2756 141 0.2618 0.3055 REMARK 3 27 1.7911 - 1.7687 1.00 2737 142 0.2799 0.3040 REMARK 3 28 1.7687 - 1.7474 1.00 2764 158 0.2932 0.2886 REMARK 3 29 1.7474 - 1.7271 0.98 2700 141 0.3047 0.3424 REMARK 3 30 1.7271 - 1.7077 0.71 1972 91 0.3293 0.3115 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 : 0.40 REMARK 3 B_SOL : 59.95 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.09 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.06160 REMARK 3 B22 (A**2) : 2.06160 REMARK 3 B33 (A**2) : -4.12320 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 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 : 0.007 3489 REMARK 3 ANGLE : 1.017 4732 REMARK 3 CHIRALITY : 0.066 524 REMARK 3 PLANARITY : 0.004 613 REMARK 3 DIHEDRAL : 17.532 1288 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 3O7U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060774. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86951 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.708 REMARK 200 RESOLUTION RANGE LOW (A) : 39.208 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: BALBES REMARK 200 STARTING MODEL: 1K6W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% PENTAERYTHRITOL PROPOXYLATE, 0.05M REMARK 280 HEPES, 0.2M POTASSIUM CHLORIDE, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-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 0.00000 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 0.00000 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 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 72.60600 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 41.91909 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 66.86967 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 72.60600 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 41.91909 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 66.86967 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 72.60600 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 41.91909 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 66.86967 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 72.60600 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 41.91909 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 66.86967 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 72.60600 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 41.91909 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 66.86967 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 72.60600 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 41.91909 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 66.86967 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 83.83819 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 133.73933 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 83.83819 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 133.73933 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 83.83819 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 133.73933 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 83.83819 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 133.73933 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 83.83819 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 133.73933 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 83.83819 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 133.73933 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 40090 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 75160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -102.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 -0.500000 -0.866025 0.000000 -72.60600 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 125.75728 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 -145.21200 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -0.500000 0.866025 0.000000 -145.21200 REMARK 350 BIOMT2 4 0.866025 0.500000 0.000000 83.83819 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -66.86967 REMARK 350 BIOMT1 5 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 -1.000000 0.000000 83.83819 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 -66.86967 REMARK 350 BIOMT1 6 -0.500000 -0.866025 0.000000 -72.60600 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 -41.91909 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 -66.86967 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 ZN ZN A 429 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 522 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 524 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 618 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 637 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 647 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 0 REMARK 465 SER A 1 REMARK 465 ASN A 2 REMARK 465 ASN A 3 REMARK 465 ARG A 426 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 ASP A 127 110.57 -166.39 REMARK 500 ILE A 183 67.41 -152.41 REMARK 500 HIS A 246 -73.88 76.10 REMARK 500 THR A 247 42.46 39.72 REMARK 500 THR A 288 -93.15 -94.00 REMARK 500 ASP A 313 -62.79 77.82 REMARK 500 TYR A 320 113.92 -161.42 REMARK 500 LEU A 322 -165.93 -128.88 REMARK 500 THR A 354 -92.43 -130.18 REMARK 500 LEU A 416 -121.87 -97.42 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 428 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 61 NE2 REMARK 620 2 HIS A 63 NE2 118.2 REMARK 620 3 HIS A 214 NE2 95.9 103.3 REMARK 620 4 O7U A 430 O4 121.1 115.5 94.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 429 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 97 NE2 REMARK 620 2 HIS A 97 NE2 0.0 REMARK 620 3 GLU A 138 OE1 89.2 89.2 REMARK 620 4 GLU A 138 OE2 113.3 113.3 57.3 REMARK 620 5 GLU A 138 OE1 89.2 89.2 0.0 57.3 REMARK 620 6 GLU A 138 OE2 113.3 113.3 57.3 0.0 57.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PXN A 427 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 428 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 429 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE O7U A 430 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 431 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 432 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 433 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 434 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 435 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 436 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PEG A 438 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1K6W RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN APO FORM DBREF 3O7U A 0 426 UNP Q53ZC8 Q53ZC8_ECOLX 1 427 SEQRES 1 A 427 MET SER ASN ASN ALA LEU GLN THR ILE ILE ASN ALA ARG SEQRES 2 A 427 LEU PRO GLY GLU GLU GLY LEU TRP GLN ILE HIS LEU GLN SEQRES 3 A 427 ASP GLY LYS ILE SER ALA ILE ASP ALA GLN SER GLY VAL SEQRES 4 A 427 MET PRO ILE THR GLU ASN SER LEU ASP ALA GLU GLN GLY SEQRES 5 A 427 LEU VAL ILE PRO PRO PHE VAL GLU PRO HIS ILE HIS LEU SEQRES 6 A 427 ASP THR THR GLN THR ALA GLY GLN PRO ASN TRP ASN GLN SEQRES 7 A 427 SER GLY THR LEU PHE GLU GLY ILE GLU ARG TRP ALA GLU SEQRES 8 A 427 ARG LYS ALA LEU LEU THR HIS ASP ASP VAL LYS GLN ARG SEQRES 9 A 427 ALA TRP GLN THR LEU LYS TRP GLN ILE ALA ASN GLY ILE SEQRES 10 A 427 GLN HIS VAL ARG THR HIS VAL ASP VAL SER ASP ALA THR SEQRES 11 A 427 LEU THR ALA LEU LYS ALA MET LEU GLU VAL LYS GLN GLU SEQRES 12 A 427 VAL ALA PRO TRP ILE ASP LEU GLN ILE VAL ALA PHE PRO SEQRES 13 A 427 GLN GLU GLY ILE LEU SER TYR PRO ASN GLY GLU ALA LEU SEQRES 14 A 427 LEU GLU GLU ALA LEU ARG LEU GLY ALA ASP VAL VAL GLY SEQRES 15 A 427 ALA ILE PRO HIS PHE GLU PHE THR ARG GLU TYR GLY VAL SEQRES 16 A 427 GLU SER LEU HIS LYS THR PHE ALA LEU ALA GLN LYS TYR SEQRES 17 A 427 ASP ARG LEU ILE ASP VAL HIS CYS ASP GLU ILE ASP ASP SEQRES 18 A 427 GLU GLN SER ARG PHE VAL GLU THR VAL ALA ALA LEU ALA SEQRES 19 A 427 HIS HIS GLU GLY MET GLY ALA ARG VAL THR ALA SER HIS SEQRES 20 A 427 THR THR ALA MET HIS SER TYR ASN GLY ALA TYR THR SER SEQRES 21 A 427 ARG LEU PHE ARG LEU LEU LYS MET SER GLY ILE ASN PHE SEQRES 22 A 427 VAL ALA ASN PRO LEU VAL ASN ILE HIS LEU GLN GLY ARG SEQRES 23 A 427 PHE ASP THR TYR PRO LYS ARG ARG GLY ILE THR ARG VAL SEQRES 24 A 427 LYS GLU MET LEU GLU SER GLY ILE ASN VAL CYS PHE GLY SEQRES 25 A 427 HIS ASP ASP VAL PHE ASP PRO TRP TYR PRO LEU GLY THR SEQRES 26 A 427 ALA ASN MET LEU GLN VAL LEU HIS MET GLY LEU HIS VAL SEQRES 27 A 427 CYS GLN LEU MET GLY TYR GLY GLN ILE ASN ASP GLY LEU SEQRES 28 A 427 ASN LEU ILE THR HIS HIS SER ALA ARG THR LEU ASN LEU SEQRES 29 A 427 GLN ASP TYR GLY ILE ALA ALA GLY ASN SER ALA ASN LEU SEQRES 30 A 427 ILE ILE LEU PRO ALA GLU ASN GLY PHE ASP ALA LEU ARG SEQRES 31 A 427 ARG GLN VAL PRO VAL ARG TYR SER VAL ARG GLY GLY LYS SEQRES 32 A 427 VAL ILE ALA SER THR GLN PRO ALA GLN THR THR VAL TYR SEQRES 33 A 427 LEU GLU GLN PRO GLU ALA ILE ASP TYR LYS ARG HET PXN A 427 25 HET ZN A 428 1 HET ZN A 429 1 HET O7U A 430 9 HET GOL A 431 6 HET GOL A 432 6 HET GOL A 433 6 HET GOL A 434 6 HET GOL A 435 6 HET GOL A 436 6 HET PEG A 437 7 HET PEG A 438 7 HETNAM PXN (2S)-1-[3-{[(2R)-2-HYDROXYPROPYL]OXY}-2,2-BIS({[(2R)-2- HETNAM 2 PXN HYDROXYPROPYL]OXY}METHYL)PROPOXY]PROPAN-2-OL HETNAM ZN ZINC ION HETNAM O7U (2R)-2-AMINO-2,5-DIHYDRO-1,5,2-DIAZAPHOSPHININ-6(1H)- HETNAM 2 O7U ONE 2-OXIDE HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN PXN PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH) HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 PXN C17 H36 O8 FORMUL 3 ZN 2(ZN 2+) FORMUL 5 O7U C3 H6 N3 O2 P FORMUL 6 GOL 6(C3 H8 O3) FORMUL 12 PEG 2(C4 H10 O3) FORMUL 14 HOH *253(H2 O) HELIX 1 1 THR A 80 ALA A 93 1 14 HELIX 2 2 THR A 96 ASN A 114 1 19 HELIX 3 3 LEU A 130 ALA A 144 1 15 HELIX 4 4 ASN A 164 GLY A 176 1 13 HELIX 5 5 ILE A 183 GLU A 187 5 5 HELIX 6 6 THR A 189 ASP A 208 1 20 HELIX 7 7 ARG A 224 GLY A 237 1 14 HELIX 8 8 MET A 238 ALA A 240 5 3 HELIX 9 9 THR A 248 TYR A 253 5 6 HELIX 10 10 ASN A 254 GLY A 269 1 16 HELIX 11 11 ASN A 275 GLN A 283 1 9 HELIX 12 12 ARG A 297 SER A 304 1 8 HELIX 13 13 ASN A 326 CYS A 338 1 13 HELIX 14 14 GLY A 342 ASP A 348 1 7 HELIX 15 15 GLY A 349 ILE A 353 5 5 HELIX 16 16 THR A 354 LEU A 361 1 8 HELIX 17 17 ASN A 383 GLN A 391 1 9 SHEET 1 A 4 LYS A 28 ALA A 34 0 SHEET 2 A 4 TRP A 20 GLN A 25 -1 N HIS A 23 O ALA A 31 SHEET 3 A 4 THR A 7 ALA A 11 -1 N ILE A 8 O ILE A 22 SHEET 4 A 4 SER A 45 ASP A 47 1 O LEU A 46 N THR A 7 SHEET 1 B 4 LEU A 52 ILE A 54 0 SHEET 2 B 4 LEU A 376 LEU A 379 -1 O LEU A 379 N LEU A 52 SHEET 3 B 4 TYR A 396 ARG A 399 -1 O VAL A 398 N LEU A 376 SHEET 4 B 4 LYS A 402 SER A 406 -1 O LYS A 402 N ARG A 399 SHEET 1 C 8 PHE A 57 ILE A 62 0 SHEET 2 C 8 ILE A 116 ASP A 124 1 O ARG A 120 N GLU A 59 SHEET 3 C 8 ASP A 148 PHE A 154 1 O GLN A 150 N VAL A 119 SHEET 4 C 8 VAL A 179 VAL A 180 1 O VAL A 179 N ALA A 153 SHEET 5 C 8 LEU A 210 CYS A 215 1 O LEU A 210 N VAL A 180 SHEET 6 C 8 VAL A 242 HIS A 246 1 O SER A 245 N VAL A 213 SHEET 7 C 8 ASN A 271 ALA A 274 1 O ASN A 271 N ALA A 244 SHEET 8 C 8 VAL A 308 PHE A 310 1 O CYS A 309 N ALA A 274 SHEET 1 D 2 THR A 412 TYR A 415 0 SHEET 2 D 2 PRO A 419 ILE A 422 -1 O GLU A 420 N VAL A 414 LINK NE2 HIS A 61 ZN ZN A 428 1555 1555 2.11 LINK NE2 HIS A 63 ZN ZN A 428 1555 1555 2.05 LINK NE2 HIS A 97 ZN ZN A 429 1555 1555 2.14 LINK NE2 HIS A 97 ZN ZN A 429 1555 5555 2.14 LINK OE1 GLU A 138 ZN ZN A 429 1555 1555 2.43 LINK OE2 GLU A 138 ZN ZN A 429 1555 1555 2.12 LINK OE1 GLU A 138 ZN ZN A 429 1555 5555 2.43 LINK OE2 GLU A 138 ZN ZN A 429 1555 5555 2.12 LINK NE2 HIS A 214 ZN ZN A 428 1555 1555 2.12 LINK ZN ZN A 428 O4 O7U A 430 1555 1555 2.06 CISPEP 1 GLN A 72 PRO A 73 0 -5.62 CISPEP 2 TYR A 289 PRO A 290 0 -0.59 SITE 1 AC1 5 GLN A 102 TRP A 105 GLN A 106 LYS A 109 SITE 2 AC1 5 GLU A 417 SITE 1 AC2 5 HIS A 61 HIS A 63 HIS A 214 ASP A 313 SITE 2 AC2 5 O7U A 430 SITE 1 AC3 2 HIS A 97 GLU A 138 SITE 1 AC4 12 HIS A 61 HIS A 63 LEU A 81 GLN A 156 SITE 2 AC4 12 HIS A 214 GLU A 217 HIS A 246 ASP A 313 SITE 3 AC4 12 ASP A 314 TRP A 319 ZN A 428 HOH A 449 SITE 1 AC5 6 LEU A 160 PRO A 163 PHE A 188 HIS A 234 SITE 2 AC5 6 HIS A 235 HOH A 461 SITE 1 AC6 8 ARG A 390 TYR A 424 HOH A 533 HOH A 593 SITE 2 AC6 8 HOH A 614 HOH A 661 HOH A 677 HOH A 680 SITE 1 AC7 5 GLN A 345 ASP A 348 ASN A 351 LEU A 352 SITE 2 AC7 5 HOH A 665 SITE 1 AC8 5 THR A 258 SER A 259 GLU A 300 HOH A 546 SITE 2 AC8 5 HOH A 671 SITE 1 AC9 2 GLN A 205 ASP A 208 SITE 1 BC1 6 GLU A 49 GLN A 50 PRO A 380 ALA A 381 SITE 2 BC1 6 GLU A 382 LYS A 425 SITE 1 BC2 3 GLN A 72 PRO A 73 LEU A 94 CRYST1 145.212 145.212 200.609 90.00 90.00 120.00 H 3 2 18 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 0.006886 0.003976 0.000000 0.00000 SCALE2 0.000000 0.007952 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004985 0.00000