PDB Short entry for 2FR6 HEADER HYDROLASE 19-JAN-06 2FR6 TITLE CRYSTAL STRUCTURE OF MOUSE CYTIDINE DEAMINASE COMPLEXED WITH CYTIDINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTIDINE DEAMINASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: CYTIDINE AMINOHYDROLASE; COMPND 5 EC: 3.5.4.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-21C KEYWDS CYTIDINE DEAMINASE, ZINC, CYTIDINE, URIDINE, PROTEIN-SUBSTRATE KEYWDS 2 COMPLEX, SUBSTRATE-PRODUCT INTERMEDIATE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.H.TEH REVDAT 3 18-OCT-17 2FR6 1 REMARK REVDAT 2 24-FEB-09 2FR6 1 VERSN REVDAT 1 11-JUL-06 2FR6 0 JRNL AUTH A.H.TEH,M.KIMURA,M.YAMAMOTO,N.TANAKA,I.YAMAGUCHI,T.KUMASAKA JRNL TITL THE 1.48 A RESOLUTION CRYSTAL STRUCTURE OF THE JRNL TITL 2 HOMOTETRAMERIC CYTIDINE DEAMINASE FROM MOUSE JRNL REF BIOCHEMISTRY V. 45 7825 2006 JRNL REFN ISSN 0006-2960 JRNL PMID 16784234 JRNL DOI 10.1021/BI060345F REMARK 2 REMARK 2 RESOLUTION. 2.07 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) : 2.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 90351.289 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 42417 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 : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2130 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 2.07 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.20 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6543 REMARK 3 BIN R VALUE (WORKING SET) : 0.2460 REMARK 3 BIN FREE R VALUE : 0.2830 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 369 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4203 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 78 REMARK 3 SOLVENT ATOMS : 358 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 17.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.60 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.00000 REMARK 3 B22 (A**2) : 4.97000 REMARK 3 B33 (A**2) : -3.97000 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) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.24 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) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.28 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.140 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.710 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.230 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.840 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 69.42 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 : CYT.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : CYT.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: DUE TO EXCESSIVE ELECTRON DENSITY, NH1 REMARK 3 OF ARG 68 WAS REFINED WITH UNIT OCCUPANCY FOR BOTH ALTERNATE REMARK 3 CONFORMATIONS IN THE FOUR SUBUNITS. DISORDERED ATOMS WERE REMARK 3 REFINED WITH ZERO OCCUPANCY. REMARK 4 REMARK 4 2FR6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JAN-06. REMARK 100 THE DEPOSITION ID IS D_1000036213. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.0 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : R-AXIS REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.1SSI REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42537 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.070 REMARK 200 RESOLUTION RANGE LOW (A) : 33.590 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.53 REMARK 200 R MERGE FOR SHELL (I) : 0.34500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2FR5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.9M AMMONIUM SULPHATE, 0.1M CITRATE, REMARK 280 PH 4.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+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 0.00000 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 0.00000 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 41.09950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.48050 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 90.36850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 41.09950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.48050 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 90.36850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 41.09950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.48050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 90.36850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 41.09950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.48050 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 90.36850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: THE BIOLOGICAL ASSEMBLY IS SIMILAR TO THE TETRAMER REMARK 300 CONTAINED IN THE ASYMMETRIC UNIT. 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: 12730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19840 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -224.0 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 28310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -486.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 82.19900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16300 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 49190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -335.0 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 82.19900 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 41.09950 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 -46.48050 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 90.36850 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 41.09950 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 46.48050 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 90.36850 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 S SO4 A1005 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1060 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 ALA A 2 REMARK 465 GLN A 3 REMARK 465 GLU A 4 REMARK 465 ARG A 5 REMARK 465 PRO A 6 REMARK 465 SER A 7 REMARK 465 CYS A 8 REMARK 465 ALA A 9 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 GLN B 3 REMARK 465 GLU B 4 REMARK 465 ARG B 5 REMARK 465 PRO B 6 REMARK 465 SER B 7 REMARK 465 CYS B 8 REMARK 465 ALA B 9 REMARK 465 ILE B 145 REMARK 465 GLN B 146 REMARK 465 MET C 1 REMARK 465 ALA C 2 REMARK 465 GLN C 3 REMARK 465 GLU C 4 REMARK 465 ARG C 5 REMARK 465 PRO C 6 REMARK 465 SER C 7 REMARK 465 CYS C 8 REMARK 465 GLN C 143 REMARK 465 LYS C 144 REMARK 465 ILE C 145 REMARK 465 GLN C 146 REMARK 465 MET D 1 REMARK 465 ALA D 2 REMARK 465 GLN D 3 REMARK 465 GLU D 4 REMARK 465 ARG D 5 REMARK 465 PRO D 6 REMARK 465 SER D 7 REMARK 465 CYS D 8 REMARK 465 ALA D 9 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 23 NE CZ NH1 NH2 REMARK 480 GLN A 146 CD OE1 NE2 REMARK 480 GLU B 11 CG CD OE1 OE2 REMARK 480 ARG B 35 NE CZ NH1 NH2 REMARK 480 ASP B 112 CG OD1 OD2 REMARK 480 GLU B 140 CG CD OE1 OE2 REMARK 480 GLN B 143 CD OE1 NE2 REMARK 480 GLU C 11 CG CD OE1 OE2 REMARK 480 LYS C 27 CD CE NZ REMARK 480 ARG C 35 NE CZ NH1 NH2 REMARK 480 ARG C 83 CD NE CZ NH1 NH2 REMARK 480 ASP C 112 CG OD1 OD2 REMARK 480 GLU C 140 CG CD OE1 OE2 REMARK 480 GLU D 93 CB CG CD OE1 OE2 REMARK 480 GLU D 94 CD OE1 OE2 REMARK 480 GLU D 140 CG CD OE1 OE2 REMARK 480 GLN D 143 CD OE1 NE2 REMARK 480 LYS D 144 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 GLN A 72 NE2 GLN D 72 1.92 REMARK 500 NE2 GLN B 72 OE1 GLN C 72 1.99 REMARK 500 C4 URI B 1002 N NH3 B 1006 2.10 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 ASP A 112 54.52 -101.18 REMARK 500 CYS C 31 59.06 -140.56 REMARK 500 ASP C 112 46.53 -93.39 REMARK 500 GLU D 93 70.06 -115.99 REMARK 500 GLU D 94 125.44 169.18 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 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 HOH A1006 O 105.6 REMARK 620 3 CYS A 99 SG 118.6 100.8 REMARK 620 4 CYS A 102 SG 109.1 100.8 118.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 102 SG REMARK 620 2 URI B1002 O4 105.0 REMARK 620 3 CYS B 99 SG 118.7 98.5 REMARK 620 4 CYS B 65 SG 110.3 102.3 118.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 99 SG REMARK 620 2 HOH C1004 O 97.6 REMARK 620 3 CYS C 102 SG 119.4 100.6 REMARK 620 4 CYS C 65 SG 117.2 109.5 109.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN D 147 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS D 99 SG REMARK 620 2 HOH D1005 O 103.0 REMARK 620 3 CYS D 65 SG 116.6 104.0 REMARK 620 4 CYS D 102 SG 121.4 100.2 108.5 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 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN D 147 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE URI B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTN C 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CTN D 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NH3 B 1006 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2FR5 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH TETRAHYDROURIDINE. REMARK 900 RELATED ID: 1ZAB RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH 3-DEAZAURIDINE. DBREF 2FR6 A 1 146 UNP P56389 CDD_MOUSE 1 146 DBREF 2FR6 B 1 146 UNP P56389 CDD_MOUSE 1 146 DBREF 2FR6 C 1 146 UNP P56389 CDD_MOUSE 1 146 DBREF 2FR6 D 1 146 UNP P56389 CDD_MOUSE 1 146 SEQRES 1 A 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 A 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 A 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 A 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 A 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 A 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 A 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 A 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 A 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 A 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 A 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 A 146 LYS ILE GLN SEQRES 1 B 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 B 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 B 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 B 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 B 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 B 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 B 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 B 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 B 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 B 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 B 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 B 146 LYS ILE GLN SEQRES 1 C 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 C 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 C 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 C 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 C 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 C 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 C 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 C 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 C 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 C 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 C 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 C 146 LYS ILE GLN SEQRES 1 D 146 MET ALA GLN GLU ARG PRO SER CYS ALA VAL GLU PRO GLU SEQRES 2 D 146 HIS VAL GLN ARG LEU LEU LEU SER SER ARG GLU ALA LYS SEQRES 3 D 146 LYS SER ALA TYR CYS PRO TYR SER ARG PHE PRO VAL GLY SEQRES 4 D 146 ALA ALA LEU LEU THR GLY ASP GLY ARG ILE PHE SER GLY SEQRES 5 D 146 CYS ASN ILE GLU ASN ALA CYS TYR PRO LEU GLY VAL CYS SEQRES 6 D 146 ALA GLU ARG THR ALA ILE GLN LYS ALA ILE SER GLU GLY SEQRES 7 D 146 TYR LYS ASP PHE ARG ALA ILE ALA ILE SER SER ASP LEU SEQRES 8 D 146 GLN GLU GLU PHE ILE SER PRO CYS GLY ALA CYS ARG GLN SEQRES 9 D 146 VAL MET ARG GLU PHE GLY THR ASP TRP ALA VAL TYR MET SEQRES 10 D 146 THR LYS PRO ASP GLY THR PHE VAL VAL ARG THR VAL GLN SEQRES 11 D 146 GLU LEU LEU PRO ALA SER PHE GLY PRO GLU ASP LEU GLN SEQRES 12 D 146 LYS ILE GLN HET ZN A 147 1 HET SO4 A1005 5 HET CTN A1001 17 HET ZN B 147 1 HET URI B1002 17 HET NH3 B1006 1 HET ZN C 147 1 HET CTN C1003 17 HET ZN D 147 1 HET CTN D1004 17 HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION HETNAM CTN 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE HETNAM URI URIDINE HETNAM NH3 AMMONIA HETSYN CTN CYTIDINE FORMUL 5 ZN 4(ZN 2+) FORMUL 6 SO4 O4 S 2- FORMUL 7 CTN 3(C9 H13 N3 O5) FORMUL 9 URI C9 H12 N2 O6 FORMUL 10 NH3 H3 N FORMUL 15 HOH *358(H2 O) HELIX 1 1 PRO A 12 LYS A 26 1 15 HELIX 2 2 LYS A 27 ALA A 29 5 3 HELIX 3 3 CYS A 59 GLY A 63 5 5 HELIX 4 4 CYS A 65 GLU A 77 1 13 HELIX 5 5 CYS A 99 PHE A 109 1 11 HELIX 6 6 VAL A 129 LEU A 133 1 5 HELIX 7 7 GLY A 138 GLN A 143 5 6 HELIX 8 8 GLU B 11 LYS B 26 1 16 HELIX 9 9 LYS B 27 ALA B 29 5 3 HELIX 10 10 CYS B 59 GLY B 63 5 5 HELIX 11 11 CYS B 65 GLU B 77 1 13 HELIX 12 12 CYS B 99 PHE B 109 1 11 HELIX 13 13 VAL B 129 LEU B 133 1 5 HELIX 14 14 GLY B 138 GLN B 143 5 6 HELIX 15 15 GLU C 11 LYS C 26 1 16 HELIX 16 16 LYS C 27 ALA C 29 5 3 HELIX 17 17 CYS C 59 GLY C 63 5 5 HELIX 18 18 CYS C 65 GLU C 77 1 13 HELIX 19 19 CYS C 99 GLU C 108 1 10 HELIX 20 20 VAL C 129 LEU C 133 1 5 HELIX 21 21 GLY C 138 LEU C 142 5 5 HELIX 22 22 PRO D 12 LYS D 26 1 15 HELIX 23 23 LYS D 27 ALA D 29 5 3 HELIX 24 24 CYS D 59 GLY D 63 5 5 HELIX 25 25 CYS D 65 GLU D 77 1 13 HELIX 26 26 CYS D 99 PHE D 109 1 11 HELIX 27 27 VAL D 129 LEU D 133 1 5 HELIX 28 28 GLY D 138 GLN D 143 5 6 SHEET 1 A 5 ILE A 49 CYS A 53 0 SHEET 2 A 5 VAL A 38 THR A 44 -1 N LEU A 42 O PHE A 50 SHEET 3 A 5 PHE A 82 SER A 89 -1 O ALA A 84 N LEU A 43 SHEET 4 A 5 ALA A 114 THR A 118 1 O TYR A 116 N ILE A 85 SHEET 5 A 5 PHE A 124 THR A 128 -1 O VAL A 125 N MET A 117 SHEET 1 B 5 ILE B 49 CYS B 53 0 SHEET 2 B 5 VAL B 38 THR B 44 -1 N LEU B 42 O PHE B 50 SHEET 3 B 5 PHE B 82 SER B 89 -1 O ALA B 84 N LEU B 43 SHEET 4 B 5 ALA B 114 THR B 118 1 O TYR B 116 N ILE B 85 SHEET 5 B 5 PHE B 124 THR B 128 -1 O VAL B 125 N MET B 117 SHEET 1 C 5 ILE C 49 CYS C 53 0 SHEET 2 C 5 VAL C 38 THR C 44 -1 N LEU C 42 O PHE C 50 SHEET 3 C 5 PHE C 82 SER C 89 -1 O ARG C 83 N LEU C 43 SHEET 4 C 5 ALA C 114 THR C 118 1 O TYR C 116 N ILE C 85 SHEET 5 C 5 PHE C 124 THR C 128 -1 O VAL C 125 N MET C 117 SHEET 1 D 5 ILE D 49 CYS D 53 0 SHEET 2 D 5 VAL D 38 THR D 44 -1 N LEU D 42 O PHE D 50 SHEET 3 D 5 PHE D 82 SER D 89 -1 O ALA D 84 N LEU D 43 SHEET 4 D 5 ALA D 114 THR D 118 1 O TYR D 116 N ILE D 85 SHEET 5 D 5 PHE D 124 THR D 128 -1 O VAL D 125 N MET D 117 LINK ZN ZN A 147 SG CYS A 65 1555 1555 2.35 LINK ZN ZN A 147 O HOH A1006 1555 1555 2.18 LINK ZN ZN A 147 SG CYS A 99 1555 1555 2.38 LINK ZN ZN A 147 SG CYS A 102 1555 1555 2.32 LINK ZN ZN B 147 SG CYS B 102 1555 1555 2.34 LINK ZN ZN B 147 O4 URI B1002 1555 1555 2.44 LINK ZN ZN B 147 SG CYS B 99 1555 1555 2.40 LINK ZN ZN B 147 SG CYS B 65 1555 1555 2.43 LINK ZN ZN C 147 SG CYS C 99 1555 1555 2.38 LINK ZN ZN C 147 O HOH C1004 1555 1555 2.29 LINK ZN ZN C 147 SG CYS C 102 1555 1555 2.38 LINK ZN ZN C 147 SG CYS C 65 1555 1555 2.35 LINK ZN ZN D 147 SG CYS D 99 1555 1555 2.44 LINK ZN ZN D 147 O HOH D1005 1555 1555 2.24 LINK ZN ZN D 147 SG CYS D 65 1555 1555 2.41 LINK ZN ZN D 147 SG CYS D 102 1555 1555 2.34 SITE 1 AC1 4 CYS A 65 CYS A 99 CYS A 102 HOH A1006 SITE 1 AC2 4 CYS B 65 CYS B 99 CYS B 102 URI B1002 SITE 1 AC3 4 CYS C 65 CYS C 99 CYS C 102 HOH C1004 SITE 1 AC4 4 CYS D 65 CYS D 99 CYS D 102 HOH D1005 SITE 1 AC5 6 GLN A 130 PRO A 134 ALA A 135 SER A 136 SITE 2 AC5 6 HOH A1008 HOH A1088 SITE 1 AC6 14 PHE A 36 VAL A 38 ASN A 54 GLU A 56 SITE 2 AC6 14 CYS A 65 ALA A 66 GLU A 67 SER A 97 SITE 3 AC6 14 HOH A1006 HOH A1037 PHE B 137 ALA C 58 SITE 4 AC6 14 CYS C 59 PRO C 61 SITE 1 AC7 17 PHE A 137 PHE B 36 VAL B 38 ASN B 54 SITE 2 AC7 17 GLU B 56 VAL B 64 CYS B 65 ALA B 66 SITE 3 AC7 17 GLU B 67 CYS B 99 ZN B 147 NH3 B1006 SITE 4 AC7 17 HOH B1022 ALA D 58 CYS D 59 TYR D 60 SITE 5 AC7 17 PRO D 61 SITE 1 AC8 16 ALA A 58 CYS A 59 TYR A 60 PRO A 61 SITE 2 AC8 16 PHE C 36 VAL C 38 ASN C 54 GLU C 56 SITE 3 AC8 16 VAL C 64 CYS C 65 ALA C 66 GLU C 67 SITE 4 AC8 16 SER C 97 HOH C1004 HOH C1029 PHE D 137 SITE 1 AC9 15 ALA B 58 CYS B 59 TYR B 60 PRO B 61 SITE 2 AC9 15 PHE C 137 PHE D 36 VAL D 38 ASN D 54 SITE 3 AC9 15 GLU D 56 CYS D 65 ALA D 66 GLU D 67 SITE 4 AC9 15 SER D 97 HOH D1005 HOH D1077 SITE 1 BC1 4 GLU B 67 ILE B 96 SER B 97 URI B1002 CRYST1 82.199 92.961 180.737 90.00 90.00 90.00 I 2 2 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 0.012166 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010757 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005533 0.00000