HEADER OXIDOREDUCTASE 31-MAY-07 2Q4S TITLE ENSEMBLE REFINEMENT OF THE PROTEIN CRYSTAL STRUCTURE OF CYSTEINE TITLE 2 DIOXYGENASE TYPE I FROM MUS MUSCULUS MM.241056 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE DIOXYGENASE TYPE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYSTEINE DIOXYGENASE TYPE I, CDO, CDO-I; COMPND 5 EC: 1.13.11.20; 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 GENE: CDO1, MM.241056; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834 P(RARE2); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PVP16 KEYWDS ENSEMBLE REFINEMENT, REFINEMENT METHODOLOGY DEVELOPMENT, MM.241056, KEYWDS 2 PFAM05995.2 CDO_I, BC013638, CUPIN FAMILY, STRUCTURAL GENOMICS, KEYWDS 3 PROTEIN STRUCTURE INITIATIVE, PSI, CENTER FOR EUKARYOTIC STRUCTURAL KEYWDS 4 GENOMICS, CESG, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION NUMMDL 16 AUTHOR E.J.LEVIN,D.A.KONDRASHOV,G.E.WESENBERG,G.N.PHILLIPS JR.,CENTER FOR AUTHOR 2 EUKARYOTIC STRUCTURAL GENOMICS (CESG) REVDAT 7 13-NOV-24 2Q4S 1 REMARK REVDAT 6 15-NOV-23 2Q4S 1 REMARK REVDAT 5 30-AUG-23 2Q4S 1 REMARK SEQADV LINK REVDAT 4 10-AUG-11 2Q4S 1 REMARK REVDAT 3 24-FEB-09 2Q4S 1 VERSN REVDAT 2 02-OCT-07 2Q4S 1 JRNL REVDAT 1 19-JUN-07 2Q4S 0 JRNL AUTH E.J.LEVIN,D.A.KONDRASHOV,G.E.WESENBERG,G.N.PHILLIPS JRNL TITL ENSEMBLE REFINEMENT OF PROTEIN CRYSTAL STRUCTURES: JRNL TITL 2 VALIDATION AND APPLICATION. JRNL REF STRUCTURE V. 15 1040 2007 JRNL REFN ISSN 0969-2126 JRNL PMID 17850744 JRNL DOI 10.1016/J.STR.2007.06.019 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.G.MCCOY,L.J.BAILEY,E.BITTO,C.A.BINGMAN,D.J.ACETI,B.G.FOX, REMARK 1 AUTH 2 G.N.PHILLIPS REMARK 1 TITL STRUCTURE AND MECHANISM OF MOUSE CYSTEINE DIOXYGENASE. REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 103 3084 2006 REMARK 1 REFN ISSN 0027-8424 REMARK 1 PMID 16492780 REMARK 1 DOI 10.1073/PNAS.0509262103 REMARK 2 REMARK 2 RESOLUTION. 1.75 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 : MAXIMUM LIKELIHOOD USING AMPLITUDES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1876902.375 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21463 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) : 0.159 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1101 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3312 REMARK 3 BIN R VALUE (WORKING SET) : 0.1490 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 175 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1512 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 188 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.26000 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) : 0.14 REMARK 3 ESD FROM SIGMAA (A) : -0.0 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.11 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.016 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.090 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.420 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.900 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.010 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.790 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 43.21 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : EDO.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THIS PDB ENTRY IS A RE-REFINEMENT USING AN ENSEMBLE MODEL OF THE REMARK 3 PREVIOUSLY REMARK 3 DEPOSITED SINGLE-CONFORMER STRUCTURE 2ATF AND REMARK 3 THE FIRST DATA SET IN THE DEPOSITED STRUCTURE FACTOR FILE REMARK 3 FOR 2ATF ALONG WITH THE R-FREE SET DEFINED THEREIN. THE COORDINATES REMARK 3 WERE GENERATED BY AN AUTOMATED PROTOCOL FROM AN INITIAL MODEL REMARK 3 CONSISTING REMARK 3 OF 16 IDENTICAL COPIES OF THE PROTEIN AND NON-WATER REMARK 3 HETERO-ATOMS ASSIGNED FRACTIONAL OCCUPANCIES ADDING UP TO ONE, AND REMARK 3 A REMARK 3 SINGLE COPY OF THE SOLVENT MOLECULES. REFINEMENT WAS CARRIED OUT REMARK 3 WITH REMARK 3 ALL THE CONFORMERS PRESENT SIMULTANEOUSLY AND WITH THE POTENTIAL REMARK 3 ENERGY REMARK 3 TERMS CORRESPONDING TO INTERACTIONS BETWEEN THE DIFFERENT REMARK 3 CONFORMERS REMARK 3 EXCLUDED. THE HELIX AND SHEET RECORDS WERE CALCULATED USING REMARK 3 COORDINATES REMARK 3 FROM THE FIRST CONFORMER ONLY. THE STRUCTURE VISUALIZATION PROGRAM REMARK 3 PYMOL IS WELL-SUITED FOR DIRECTLY VIEWING THE ENSEMBLE MODEL REMARK 3 PRESENTED IN THIS PDB FILE. REMARK 4 REMARK 4 2Q4S COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-07. REMARK 100 THE DEPOSITION ID IS D_1000043148. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: RE-REFINEMENT USING REMARK 200 ENSEMBLE MODEL REMARK 200 SOFTWARE USED: CNS 1.1 REMARK 200 STARTING MODEL: PDB ENTRY 2ATF REMARK 200 REMARK 200 REMARK: AUTHOR USED THE SF DATA FROM ENTRY 2ATF. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 61.03800 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.77500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.77500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.55700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.77500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.77500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.51900 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.77500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.77500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.55700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.77500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.77500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.51900 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 61.03800 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: MONOMERIC 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 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 1 SER A 1 REMARK 465 1 GLU A 2 REMARK 465 1 ARG A 3 REMARK 465 1 THR A 4 REMARK 465 1 PHE A 191 REMARK 465 1 THR A 192 REMARK 465 1 THR A 193 REMARK 465 1 SER A 194 REMARK 465 1 GLY A 195 REMARK 465 1 SER A 196 REMARK 465 1 LEU A 197 REMARK 465 1 GLU A 198 REMARK 465 1 ASN A 199 REMARK 465 1 ASN A 200 REMARK 465 2 SER A 1 REMARK 465 2 GLU A 2 REMARK 465 2 ARG A 3 REMARK 465 2 THR A 4 REMARK 465 2 PHE A 191 REMARK 465 2 THR A 192 REMARK 465 2 THR A 193 REMARK 465 2 SER A 194 REMARK 465 2 GLY A 195 REMARK 465 2 SER A 196 REMARK 465 2 LEU A 197 REMARK 465 2 GLU A 198 REMARK 465 2 ASN A 199 REMARK 465 2 ASN A 200 REMARK 465 3 SER A 1 REMARK 465 3 GLU A 2 REMARK 465 3 ARG A 3 REMARK 465 3 THR A 4 REMARK 465 3 PHE A 191 REMARK 465 3 THR A 192 REMARK 465 3 THR A 193 REMARK 465 3 SER A 194 REMARK 465 3 GLY A 195 REMARK 465 3 SER A 196 REMARK 465 3 LEU A 197 REMARK 465 3 GLU A 198 REMARK 465 3 ASN A 199 REMARK 465 3 ASN A 200 REMARK 465 4 SER A 1 REMARK 465 4 GLU A 2 REMARK 465 4 ARG A 3 REMARK 465 4 THR A 4 REMARK 465 4 PHE A 191 REMARK 465 4 THR A 192 REMARK 465 4 THR A 193 REMARK 465 4 SER A 194 REMARK 465 4 GLY A 195 REMARK 465 4 SER A 196 REMARK 465 4 LEU A 197 REMARK 465 4 GLU A 198 REMARK 465 4 ASN A 199 REMARK 465 4 ASN A 200 REMARK 465 5 SER A 1 REMARK 465 5 GLU A 2 REMARK 465 5 ARG A 3 REMARK 465 5 THR A 4 REMARK 465 5 PHE A 191 REMARK 465 5 THR A 192 REMARK 465 5 THR A 193 REMARK 465 5 SER A 194 REMARK 465 5 GLY A 195 REMARK 465 5 SER A 196 REMARK 465 5 LEU A 197 REMARK 465 5 GLU A 198 REMARK 465 5 ASN A 199 REMARK 465 5 ASN A 200 REMARK 465 6 SER A 1 REMARK 465 6 GLU A 2 REMARK 465 6 ARG A 3 REMARK 465 6 THR A 4 REMARK 465 6 PHE A 191 REMARK 465 6 THR A 192 REMARK 465 6 THR A 193 REMARK 465 6 SER A 194 REMARK 465 6 GLY A 195 REMARK 465 6 SER A 196 REMARK 465 6 LEU A 197 REMARK 465 6 GLU A 198 REMARK 465 6 ASN A 199 REMARK 465 6 ASN A 200 REMARK 465 7 SER A 1 REMARK 465 7 GLU A 2 REMARK 465 7 ARG A 3 REMARK 465 7 THR A 4 REMARK 465 7 PHE A 191 REMARK 465 7 THR A 192 REMARK 465 7 THR A 193 REMARK 465 7 SER A 194 REMARK 465 7 GLY A 195 REMARK 465 7 SER A 196 REMARK 465 7 LEU A 197 REMARK 465 7 GLU A 198 REMARK 465 7 ASN A 199 REMARK 465 7 ASN A 200 REMARK 465 8 SER A 1 REMARK 465 8 GLU A 2 REMARK 465 8 ARG A 3 REMARK 465 8 THR A 4 REMARK 465 8 PHE A 191 REMARK 465 8 THR A 192 REMARK 465 8 THR A 193 REMARK 465 8 SER A 194 REMARK 465 8 GLY A 195 REMARK 465 8 SER A 196 REMARK 465 8 LEU A 197 REMARK 465 8 GLU A 198 REMARK 465 8 ASN A 199 REMARK 465 8 ASN A 200 REMARK 465 9 SER A 1 REMARK 465 9 GLU A 2 REMARK 465 9 ARG A 3 REMARK 465 9 THR A 4 REMARK 465 9 PHE A 191 REMARK 465 9 THR A 192 REMARK 465 9 THR A 193 REMARK 465 9 SER A 194 REMARK 465 9 GLY A 195 REMARK 465 9 SER A 196 REMARK 465 9 LEU A 197 REMARK 465 9 GLU A 198 REMARK 465 9 ASN A 199 REMARK 465 9 ASN A 200 REMARK 465 10 SER A 1 REMARK 465 10 GLU A 2 REMARK 465 10 ARG A 3 REMARK 465 10 THR A 4 REMARK 465 10 PHE A 191 REMARK 465 10 THR A 192 REMARK 465 10 THR A 193 REMARK 465 10 SER A 194 REMARK 465 10 GLY A 195 REMARK 465 10 SER A 196 REMARK 465 10 LEU A 197 REMARK 465 10 GLU A 198 REMARK 465 10 ASN A 199 REMARK 465 10 ASN A 200 REMARK 465 11 SER A 1 REMARK 465 11 GLU A 2 REMARK 465 11 ARG A 3 REMARK 465 11 THR A 4 REMARK 465 11 PHE A 191 REMARK 465 11 THR A 192 REMARK 465 11 THR A 193 REMARK 465 11 SER A 194 REMARK 465 11 GLY A 195 REMARK 465 11 SER A 196 REMARK 465 11 LEU A 197 REMARK 465 11 GLU A 198 REMARK 465 11 ASN A 199 REMARK 465 11 ASN A 200 REMARK 465 12 SER A 1 REMARK 465 12 GLU A 2 REMARK 465 12 ARG A 3 REMARK 465 12 THR A 4 REMARK 465 12 PHE A 191 REMARK 465 12 THR A 192 REMARK 465 12 THR A 193 REMARK 465 12 SER A 194 REMARK 465 12 GLY A 195 REMARK 465 12 SER A 196 REMARK 465 12 LEU A 197 REMARK 465 12 GLU A 198 REMARK 465 12 ASN A 199 REMARK 465 12 ASN A 200 REMARK 465 13 SER A 1 REMARK 465 13 GLU A 2 REMARK 465 13 ARG A 3 REMARK 465 13 THR A 4 REMARK 465 13 PHE A 191 REMARK 465 13 THR A 192 REMARK 465 13 THR A 193 REMARK 465 13 SER A 194 REMARK 465 13 GLY A 195 REMARK 465 13 SER A 196 REMARK 465 13 LEU A 197 REMARK 465 13 GLU A 198 REMARK 465 13 ASN A 199 REMARK 465 13 ASN A 200 REMARK 465 14 SER A 1 REMARK 465 14 GLU A 2 REMARK 465 14 ARG A 3 REMARK 465 14 THR A 4 REMARK 465 14 PHE A 191 REMARK 465 14 THR A 192 REMARK 465 14 THR A 193 REMARK 465 14 SER A 194 REMARK 465 14 GLY A 195 REMARK 465 14 SER A 196 REMARK 465 14 LEU A 197 REMARK 465 14 GLU A 198 REMARK 465 14 ASN A 199 REMARK 465 14 ASN A 200 REMARK 465 15 SER A 1 REMARK 465 15 GLU A 2 REMARK 465 15 ARG A 3 REMARK 465 15 THR A 4 REMARK 465 15 PHE A 191 REMARK 465 15 THR A 192 REMARK 465 15 THR A 193 REMARK 465 15 SER A 194 REMARK 465 15 GLY A 195 REMARK 465 15 SER A 196 REMARK 465 15 LEU A 197 REMARK 465 15 GLU A 198 REMARK 465 15 ASN A 199 REMARK 465 15 ASN A 200 REMARK 465 16 SER A 1 REMARK 465 16 GLU A 2 REMARK 465 16 ARG A 3 REMARK 465 16 THR A 4 REMARK 465 16 PHE A 191 REMARK 465 16 THR A 192 REMARK 465 16 THR A 193 REMARK 465 16 SER A 194 REMARK 465 16 GLY A 195 REMARK 465 16 SER A 196 REMARK 465 16 LEU A 197 REMARK 465 16 GLU A 198 REMARK 465 16 ASN A 199 REMARK 465 16 ASN A 200 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 9 CYS A 130 CB CYS A 130 SG 0.112 REMARK 500 10 CYS A 93 CB CYS A 93 SG 0.311 REMARK 500 12 CYS A 93 CB CYS A 93 SG 0.156 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 2 LEU A 95 CA - CB - CG ANGL. DEV. = 14.5 DEGREES REMARK 500 5 CYS A 130 CA - CB - SG ANGL. DEV. = 7.7 DEGREES REMARK 500 6 PRO A 190 C - N - CA ANGL. DEV. = 9.4 DEGREES REMARK 500 9 CYS A 130 CA - CB - SG ANGL. DEV. = 6.8 DEGREES REMARK 500 10 CYS A 93 CA - CB - SG ANGL. DEV. = 8.6 DEGREES REMARK 500 10 LEU A 95 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 11 CYS A 130 CA - CB - SG ANGL. DEV. = 9.5 DEGREES REMARK 500 13 ILE A 85 N - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 14 ILE A 85 N - CA - C ANGL. DEV. = -17.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 1 ASP A 87 -169.20 -117.56 REMARK 500 1 ASP A 111 -97.85 -69.88 REMARK 500 1 LYS A 112 -25.09 -153.20 REMARK 500 1 SER A 114 49.57 -79.47 REMARK 500 1 SER A 121 153.82 167.19 REMARK 500 1 ASN A 128 -4.28 88.04 REMARK 500 1 THR A 148 19.89 -148.35 REMARK 500 2 SER A 42 131.17 -27.75 REMARK 500 2 TRP A 47 42.58 -102.15 REMARK 500 2 LYS A 112 -70.02 -67.14 REMARK 500 2 SER A 121 165.14 175.85 REMARK 500 2 ASN A 128 -11.21 80.16 REMARK 500 3 ASP A 111 -146.95 -103.56 REMARK 500 3 LYS A 112 -91.50 -69.18 REMARK 500 3 ASN A 128 -9.45 71.73 REMARK 500 4 PRO A 110 -168.06 -64.45 REMARK 500 4 SER A 121 165.64 179.80 REMARK 500 4 ASN A 128 -18.73 73.85 REMARK 500 4 THR A 171 -20.65 -140.14 REMARK 500 5 GLU A 27 -167.69 -123.02 REMARK 500 5 ALA A 39 23.05 -76.48 REMARK 500 5 ILE A 85 118.55 -25.36 REMARK 500 5 ASN A 128 -2.92 73.59 REMARK 500 5 HIS A 140 -159.63 -118.08 REMARK 500 5 ARG A 141 25.73 -156.91 REMARK 500 5 VAL A 142 136.93 -16.46 REMARK 500 6 SER A 42 129.77 -36.11 REMARK 500 6 ALA A 51 57.09 -91.83 REMARK 500 6 ASN A 128 -15.17 74.18 REMARK 500 7 ARG A 10 -85.56 -66.93 REMARK 500 7 THR A 11 -165.14 -113.81 REMARK 500 7 ARG A 57 157.99 159.04 REMARK 500 7 ASN A 67 21.77 44.57 REMARK 500 7 ASP A 90 19.66 58.19 REMARK 500 7 PRO A 110 -175.69 -67.01 REMARK 500 7 ASP A 111 -105.50 -111.09 REMARK 500 7 LYS A 112 -15.18 -149.32 REMARK 500 7 LYS A 113 -106.08 -56.37 REMARK 500 7 SER A 114 42.81 169.73 REMARK 500 7 ASN A 128 -5.40 72.89 REMARK 500 7 THR A 148 -84.94 -107.64 REMARK 500 7 THR A 171 -58.73 -125.50 REMARK 500 8 ASN A 128 -3.64 72.70 REMARK 500 9 SER A 121 172.13 179.91 REMARK 500 9 ASN A 128 -28.55 99.81 REMARK 500 10 PRO A 44 -39.66 -39.64 REMARK 500 10 ALA A 45 -9.53 -57.81 REMARK 500 10 LEU A 62 132.60 -39.80 REMARK 500 10 ASN A 67 39.27 37.92 REMARK 500 10 LYS A 113 135.51 -171.83 REMARK 500 REMARK 500 THIS ENTRY HAS 97 RAMACHANDRAN OUTLIERS. 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 NI A 201 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 86 NE2 REMARK 620 2 HIS A 88 NE2 95.6 REMARK 620 3 HIS A 140 NE2 91.2 94.6 REMARK 620 4 HOH A 359 O 151.1 110.6 98.4 REMARK 620 5 HOH A 360 O 95.3 166.9 92.4 57.2 REMARK 620 6 HOH A 361 O 94.9 84.0 173.9 76.7 88.0 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 NI A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 234 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: GO.35683 RELATED DB: TARGETDB REMARK 900 RELATED ID: 2ATF RELATED DB: PDB REMARK 900 ORIGINAL REFINEMENT BASED ON SAME DATA AND R-FREE SET. DBREF 2Q4S A 2 200 UNP P60334 CDO1_MOUSE 2 200 SEQADV 2Q4S SER A 1 UNP P60334 EXPRESSION TAG SEQADV 2Q4S MSE A 73 UNP P60334 MET 73 MODIFIED RESIDUE SEQADV 2Q4S MSE A 117 UNP P60334 MET 117 MODIFIED RESIDUE SEQADV 2Q4S MSE A 179 UNP P60334 MET 179 MODIFIED RESIDUE SEQRES 1 A 200 SER GLU ARG THR GLU LEU LEU LYS PRO ARG THR LEU ALA SEQRES 2 A 200 ASP LEU ILE ARG ILE LEU HIS GLU LEU PHE ALA GLY ASP SEQRES 3 A 200 GLU VAL ASN VAL GLU GLU VAL GLN ALA VAL LEU GLU ALA SEQRES 4 A 200 TYR GLU SER ASN PRO ALA GLU TRP ALA LEU TYR ALA LYS SEQRES 5 A 200 PHE ASP GLN TYR ARG TYR THR ARG ASN LEU VAL ASP GLN SEQRES 6 A 200 GLY ASN GLY LYS PHE ASN LEU MSE ILE LEU CYS TRP GLY SEQRES 7 A 200 GLU GLY HIS GLY SER SER ILE HIS ASP HIS THR ASP SER SEQRES 8 A 200 HIS CYS PHE LEU LYS LEU LEU GLN GLY ASN LEU LYS GLU SEQRES 9 A 200 THR LEU PHE ASP TRP PRO ASP LYS LYS SER ASN GLU MSE SEQRES 10 A 200 ILE LYS LYS SER GLU ARG THR LEU ARG GLU ASN GLN CYS SEQRES 11 A 200 ALA TYR ILE ASN ASP SER ILE GLY LEU HIS ARG VAL GLU SEQRES 12 A 200 ASN VAL SER HIS THR GLU PRO ALA VAL SER LEU HIS LEU SEQRES 13 A 200 TYR SER PRO PRO PHE ASP THR CYS HIS ALA PHE ASP GLN SEQRES 14 A 200 ARG THR GLY HIS LYS ASN LYS VAL THR MSE THR PHE HIS SEQRES 15 A 200 SER LYS PHE GLY ILE ARG THR PRO PHE THR THR SER GLY SEQRES 16 A 200 SER LEU GLU ASN ASN MODRES 2Q4S MSE A 73 MET SELENOMETHIONINE MODRES 2Q4S MSE A 117 MET SELENOMETHIONINE MODRES 2Q4S MSE A 179 MET SELENOMETHIONINE HET MSE A 73 8 HET MSE A 117 8 HET MSE A 179 8 HET NI A 201 1 HET EDO A 234 4 HETNAM MSE SELENOMETHIONINE HETNAM NI NICKEL (II) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 NI NI 2+ FORMUL 3 EDO C2 H6 O2 FORMUL 4 HOH *188(H2 O) HELIX 1 1 THR A 11 PHE A 23 1 13 HELIX 2 2 ASN A 29 TYR A 40 1 12 HELIX 3 3 ASN A 43 ALA A 48 1 6 HELIX 4 4 GLN A 65 LYS A 69 5 5 SHEET 1 A 6 CYS A 130 ILE A 133 0 SHEET 2 A 6 HIS A 92 GLN A 99 -1 N LEU A 95 O ALA A 131 SHEET 3 A 6 ALA A 151 SER A 158 -1 O LEU A 154 N LYS A 96 SHEET 4 A 6 ASN A 71 TRP A 77 -1 N TRP A 77 O ALA A 151 SHEET 5 A 6 ASN A 61 ASP A 64 -1 N ASP A 64 O LEU A 72 SHEET 6 A 6 SER A 183 LYS A 184 1 O SER A 183 N LEU A 62 SHEET 1 B 3 ILE A 85 HIS A 86 0 SHEET 2 B 3 THR A 163 PHE A 167 -1 O PHE A 167 N ILE A 85 SHEET 3 B 3 LYS A 174 THR A 178 -1 O VAL A 177 N CYS A 164 SHEET 1 C 3 SER A 121 LEU A 125 0 SHEET 2 C 3 LEU A 102 PHE A 107 -1 N LEU A 106 O SER A 121 SHEET 3 C 3 LEU A 139 GLU A 143 -1 O GLU A 143 N LYS A 103 LINK C LEU A 72 N MSE A 73 1555 1555 1.34 LINK C MSE A 73 N ILE A 74 1555 1555 1.34 LINK C GLU A 116 N MSE A 117 1555 1555 1.33 LINK C MSE A 117 N ILE A 118 1555 1555 1.32 LINK C THR A 178 N MSE A 179 1555 1555 1.33 LINK C MSE A 179 N THR A 180 1555 1555 1.33 LINK NE2 HIS A 86 NI NI A 201 1555 1555 1.99 LINK NE2 HIS A 88 NI NI A 201 1555 1555 2.08 LINK NE2 HIS A 140 NI NI A 201 1555 1555 2.15 LINK NI NI A 201 O HOH A 359 1555 1555 2.19 LINK NI NI A 201 O HOH A 360 1555 1555 2.29 LINK NI NI A 201 O HOH A 361 1555 1555 2.29 CISPEP 1 SER A 158 PRO A 159 1 -0.37 CISPEP 2 SER A 158 PRO A 159 2 -0.27 CISPEP 3 SER A 158 PRO A 159 3 -0.36 CISPEP 4 SER A 158 PRO A 159 4 -0.28 CISPEP 5 SER A 158 PRO A 159 5 -0.35 CISPEP 6 SER A 158 PRO A 159 6 -0.40 CISPEP 7 SER A 158 PRO A 159 7 -0.33 CISPEP 8 SER A 158 PRO A 159 8 -0.27 CISPEP 9 SER A 158 PRO A 159 9 0.04 CISPEP 10 SER A 158 PRO A 159 10 -0.42 CISPEP 11 SER A 158 PRO A 159 11 -0.43 CISPEP 12 SER A 158 PRO A 159 12 -0.29 CISPEP 13 SER A 158 PRO A 159 13 -0.62 CISPEP 14 SER A 158 PRO A 159 14 -0.81 CISPEP 15 SER A 158 PRO A 159 15 -0.06 CISPEP 16 SER A 158 PRO A 159 16 -0.48 SITE 1 AC1 6 HIS A 86 HIS A 88 HIS A 140 HOH A 359 SITE 2 AC1 6 HOH A 360 HOH A 361 SITE 1 AC2 2 ASP A 162 THR A 163 CRYST1 57.550 57.550 122.076 90.00 90.00 90.00 P 43 21 2 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 0.017376 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017376 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008192 0.00000 MODEL 1