HEADER OXIDOREDUCTASE 26-AUG-19 6U4V TITLE NON-CROSSLINKED WILD TYPE CYSTEINE DIOXYGENASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYSTEINE DIOXYGENASE TYPE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYSTEINE DIOXYGENASE TYPE I,CDO-I; COMPND 5 EC: 1.13.11.20; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: CDO1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NON-HEME, MONO-IRON, DIOXYGENASE, CYSTEINE-TYROSINE CROSSLINK, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR K.M.MENEELY,A.S.CHILTON,D.L.FORBES,H.R.ELLIS,A.L.LAMB REVDAT 2 11-OCT-23 6U4V 1 REMARK REVDAT 1 08-JUL-20 6U4V 0 JRNL AUTH D.L.FORBES,K.M.MENEELY,A.S.CHILTON,A.L.LAMB,H.R.ELLIS JRNL TITL THE 3-HIS METAL COORDINATION SITE PROMOTES THE COUPLING OF JRNL TITL 2 OXYGEN ACTIVATION TO CYSTEINE OXIDATION IN CYSTEINE JRNL TITL 3 DIOXYGENASE. JRNL REF BIOCHEMISTRY V. 59 2022 2020 JRNL REFN ISSN 0006-2960 JRNL PMID 32368901 JRNL DOI 10.1021/ACS.BIOCHEM.9B01085 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 9435 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.960 REMARK 3 FREE R VALUE TEST SET COUNT : 940 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 4.4000 - 3.5000 1.00 1259 139 0.1532 0.1887 REMARK 3 2 3.5000 - 3.0500 0.99 1225 137 0.1770 0.2240 REMARK 3 3 3.0500 - 2.7700 0.99 1217 135 0.0000 0.2847 REMARK 3 4 2.7700 - 2.5800 0.97 1194 131 0.0000 0.2433 REMARK 3 5 2.5800 - 2.4200 0.95 1151 124 0.0000 0.2890 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.218 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.534 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.29 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 : 0.012 1540 REMARK 3 ANGLE : 1.189 2084 REMARK 3 CHIRALITY : 0.057 223 REMARK 3 PLANARITY : 0.008 271 REMARK 3 DIHEDRAL : 3.241 915 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 6U4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243948. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9683 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 38.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 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: PHENIX REMARK 200 STARTING MODEL: 2B5H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES, PH 6.5, 1 M LITHIUM REMARK 280 CHLORIDE, 24% PEG 20,000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 297.15K 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 61.23450 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.79750 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.79750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 91.85175 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.79750 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.79750 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 30.61725 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.79750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.79750 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 91.85175 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.79750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.79750 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 30.61725 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 61.23450 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 ARG A 3 REMARK 465 THR A 4 REMARK 465 GLU A 5 REMARK 465 PHE A 191 REMARK 465 THR A 192 REMARK 465 THR A 193 REMARK 465 SER A 194 REMARK 465 GLY A 195 REMARK 465 SER A 196 REMARK 465 LEU A 197 REMARK 465 GLU A 198 REMARK 465 ASN A 199 REMARK 465 ASN A 200 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 ASN A 128 -4.54 76.96 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 FE A 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 86 NE2 REMARK 620 2 HIS A 88 NE2 97.6 REMARK 620 3 HIS A 140 NE2 102.4 96.9 REMARK 620 4 HOH A 419 O 124.9 118.6 111.9 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 FE A 301 DBREF 6U4V A 1 200 UNP P21816 CDO1_RAT 1 200 SEQADV 6U4V ASP A 46 UNP P21816 GLU 46 CONFLICT SEQRES 1 A 200 MET 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 ASP 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 MET 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 MET 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 MET 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 HET FE A 301 1 HETNAM FE FE (III) ION FORMUL 2 FE FE 3+ FORMUL 3 HOH *19(H2 O) HELIX 1 AA1 THR A 11 PHE A 23 1 13 HELIX 2 AA2 ASN A 29 TYR A 40 1 12 HELIX 3 AA3 ASN A 43 ALA A 48 1 6 HELIX 4 AA4 LEU A 49 ALA A 51 5 3 HELIX 5 AA5 GLN A 65 LYS A 69 5 5 SHEET 1 AA1 7 CYS A 130 ILE A 133 0 SHEET 2 AA1 7 HIS A 92 GLN A 99 -1 N LEU A 95 O ALA A 131 SHEET 3 AA1 7 ALA A 151 SER A 158 -1 O SER A 158 N HIS A 92 SHEET 4 AA1 7 ASN A 71 TRP A 77 -1 N MET A 73 O HIS A 155 SHEET 5 AA1 7 THR A 59 ASP A 64 -1 N ASN A 61 O ILE A 74 SHEET 6 AA1 7 SER A 183 LYS A 184 1 O SER A 183 N LEU A 62 SHEET 7 AA1 7 ILE A 187 ARG A 188 -1 O ILE A 187 N LYS A 184 SHEET 1 AA2 3 ILE A 85 HIS A 86 0 SHEET 2 AA2 3 THR A 163 PHE A 167 -1 O PHE A 167 N ILE A 85 SHEET 3 AA2 3 LYS A 174 THR A 178 -1 O ASN A 175 N ALA A 166 SHEET 1 AA3 3 LYS A 119 LEU A 125 0 SHEET 2 AA3 3 LEU A 102 PHE A 107 -1 N LEU A 102 O LEU A 125 SHEET 3 AA3 3 LEU A 139 GLU A 143 -1 O GLU A 143 N LYS A 103 LINK NE2 HIS A 86 FE FE A 301 1555 1555 2.04 LINK NE2 HIS A 88 FE FE A 301 1555 1555 2.10 LINK NE2 HIS A 140 FE FE A 301 1555 1555 2.07 LINK FE FE A 301 O HOH A 419 1555 1555 2.09 CISPEP 1 SER A 158 PRO A 159 0 -10.78 SITE 1 AC1 4 HIS A 86 HIS A 88 HIS A 140 HOH A 419 CRYST1 57.595 57.595 122.469 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 0.017363 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008165 0.00000