HEADER METAL BINDING PROTEIN 08-AUG-25 9PYO TITLE CRYSTAL STRUCTURE OF FE/2-OG DEPENDENT DIOXYGENASE MYSH IN COMPLEX TITLE 2 WITH IRON AND 2-OXOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: FE/2-OG DEPENDENT DIOXYGENASE MYSH; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: PROTEIN WAS EXPRESSED WITH A HEXA-HISTIDINE TAG THAT COMPND 6 WAS CLEAVED USING TEV PROTEASE BEFORE CRYSTALLIZATION SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NOSTOC LINCKIA; SOURCE 3 ORGANISM_TAXID: 92942; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS NON-HEME IRON DEPENDENT, DIOXYGENASE, JELLY ROLL FOLD, PHYTANOYL-COA, KEYWDS 2 ALPHAKETOGLUTARATE DEPENDENT, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.N.WANNIARACHCHI,S.D.BRUNER REVDAT 1 06-MAY-26 9PYO 0 JRNL AUTH T.N.WANNIARACHCHI,S.D.BRUNER JRNL TITL CRYSTAL STRUCTURE OF NON-HEME IRON AND 2-OXOGLUTARATE JRNL TITL 2 DEPENDENT DIOXYGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.22 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 37718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1924 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 26.2200 - 3.6200 1.00 2571 144 0.1484 0.1779 REMARK 3 2 3.6200 - 2.8800 1.00 2493 200 0.1814 0.2141 REMARK 3 3 2.8700 - 2.5100 1.00 2595 126 0.2170 0.2569 REMARK 3 4 2.5100 - 2.2800 1.00 2538 164 0.2181 0.2503 REMARK 3 5 2.2800 - 2.1200 1.00 2566 118 0.2267 0.2810 REMARK 3 6 2.1200 - 1.9900 1.00 2567 138 0.2366 0.2500 REMARK 3 7 1.9900 - 1.8900 1.00 2568 174 0.2536 0.2636 REMARK 3 8 1.8900 - 1.8100 1.00 2523 122 0.2316 0.2857 REMARK 3 9 1.8100 - 1.7400 1.00 2627 116 0.2322 0.3091 REMARK 3 10 1.7400 - 1.6800 1.00 2543 144 0.2475 0.2717 REMARK 3 11 1.6800 - 1.6300 1.00 2567 151 0.2483 0.3089 REMARK 3 12 1.6300 - 1.5800 1.00 2574 116 0.2614 0.2533 REMARK 3 13 1.5800 - 1.5400 1.00 2571 100 0.2612 0.2529 REMARK 3 14 1.5400 - 1.5000 0.95 2491 111 0.2817 0.3358 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.189 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.213 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.59 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 : 0.006 2098 REMARK 3 ANGLE : 0.845 2850 REMARK 3 CHIRALITY : 0.054 300 REMARK 3 PLANARITY : 0.007 368 REMARK 3 DIHEDRAL : 14.298 771 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 9PYO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-AUG-25. REMARK 100 THE DEPOSITION ID IS D_1000298799. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-NOV-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS-II REMARK 200 BEAMLINE : 17-ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9201 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75263 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 26.220 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 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 : 1.260 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX 1.21.1_5286 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE, 0.1 M REMARK 280 TRIS HYDROCHLORIDE PH 8.5, 35 % PEG 4000, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,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 35.77200 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 71.54400 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 SER A -2 REMARK 465 ASN A -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 LEU A 2 REMARK 465 LYS A 3 REMARK 465 VAL A 4 REMARK 465 ASP A 5 REMARK 465 THR A 6 REMARK 465 GLN A 7 REMARK 465 ASP A 53 REMARK 465 LYS A 54 REMARK 465 ASN A 55 REMARK 465 VAL A 56 REMARK 465 PRO A 57 REMARK 465 LYS A 58 REMARK 465 PRO A 59 REMARK 465 GLN A 60 REMARK 465 GLY A 61 REMARK 465 HIS A 266 REMARK 465 ARG A 267 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 SER A 68 31.79 72.46 REMARK 500 CYS A 257 -176.35 -174.26 REMARK 500 PHE A 260 67.89 -119.58 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 302 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 119 NE2 REMARK 620 2 ASP A 121 OD1 96.8 REMARK 620 3 HIS A 198 NE2 86.5 96.2 REMARK 620 4 AKG A 301 O2 168.7 93.5 97.1 REMARK 620 5 AKG A 301 O5 87.8 173.2 89.1 81.5 REMARK 620 6 HOH A 481 O 88.2 89.0 172.9 87.3 86.1 REMARK 620 N 1 2 3 4 5 DBREF 9PYO A -2 267 PDB 9PYO 9PYO -2 267 SEQRES 1 A 270 SER ASN ALA MET LEU LYS VAL ASP THR GLN LYS ILE SER SEQRES 2 A 270 PRO GLN GLN VAL GLU ALA PHE GLU ARG ASP GLY VAL ILE SEQRES 3 A 270 CYS VAL LYS ASN ALA VAL ASP ASP ILE TRP VAL GLU ARG SEQRES 4 A 270 MET ARG THR ALA VAL ASP LYS ASN ILE SER ILE PRO GLY SEQRES 5 A 270 PRO LEU GLU ASP LYS ASN VAL PRO LYS PRO GLN GLY SER SEQRES 6 A 270 ALA GLU HIS ALA SER SER ILE TRP LEU ILE ASP ALA ASP SEQRES 7 A 270 PHE ARG ALA LEU ALA PHE GLU SER PRO LEU PRO THR LEU SEQRES 8 A 270 ALA ALA GLN VAL LEU LYS SER LYS LYS LEU ASN PHE LEU SEQRES 9 A 270 ALA ASP GLY PHE PHE VAL LYS LYS PRO GLU SER ASN GLY SEQRES 10 A 270 ARG ILE GLY TRP HIS ASN ASP LEU PRO TYR TRP PRO VAL SEQRES 11 A 270 GLN GLY TRP GLN CYS CYS LYS ILE TRP LEU ALA LEU ASP SEQRES 12 A 270 THR VAL LYS GLN GLU ASN GLY ARG LEU GLU TYR ILE LYS SEQRES 13 A 270 GLY SER HIS GLN TRP GLY LYS GLU LEU ARG GLU ARG SER SEQRES 14 A 270 ASN PRO SER TRP PHE ILE GLU PRO GLU PRO HIS GLU ILE SEQRES 15 A 270 LEU SER TRP ASP MET GLU ALA GLY ASP CYS LEU ILE HIS SEQRES 16 A 270 HIS PHE LEU THR ILE HIS HIS SER VAL THR ASN ILE SER SEQRES 17 A 270 SER THR GLN ARG ARG ALA ILE VAL THR ASN TRP THR GLY SEQRES 18 A 270 ASP ASP VAL THR TYR TYR GLN ARG PRO LYS ALA TRP PRO SEQRES 19 A 270 PHE LYS PRO LEU GLU GLU ILE ASP LEU PRO GLU PHE ASN SEQRES 20 A 270 SER LEU LYS THR LYS LYS SER GLY GLU PRO ILE ASP CYS SEQRES 21 A 270 ASP ILE PHE PRO ARG VAL GLN VAL HIS ARG HET AKG A 301 10 HET FE A 302 1 HET EDO A 303 4 HETNAM AKG 2-OXOGLUTARIC ACID HETNAM FE FE (III) ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 AKG C5 H6 O5 FORMUL 3 FE FE 3+ FORMUL 4 EDO C2 H6 O2 FORMUL 5 HOH *219(H2 O) HELIX 1 AA1 SER A 10 GLY A 21 1 12 HELIX 2 AA2 ASP A 30 ILE A 45 1 16 HELIX 3 AA3 ILE A 69 ILE A 72 5 4 HELIX 4 AA4 ASP A 73 SER A 83 1 11 HELIX 5 AA5 PRO A 84 LYS A 94 1 11 HELIX 6 AA6 ASP A 121 TRP A 125 5 5 HELIX 7 AA7 LYS A 143 GLY A 147 5 5 HELIX 8 AA8 GLY A 154 GLY A 159 5 6 HELIX 9 AA9 GLU A 175 HIS A 177 5 3 HELIX 10 AB1 PRO A 234 ILE A 238 5 5 HELIX 11 AB2 LEU A 240 GLU A 242 5 3 HELIX 12 AB3 PHE A 243 THR A 248 1 6 SHEET 1 AA1 6 VAL A 22 VAL A 25 0 SHEET 2 AA1 6 CYS A 189 HIS A 193 -1 O CYS A 189 N VAL A 25 SHEET 3 AA1 6 CYS A 132 ALA A 138 -1 N TRP A 136 O LEU A 190 SHEET 4 AA1 6 ARG A 209 THR A 217 -1 O ILE A 212 N LEU A 137 SHEET 5 AA1 6 ASN A 99 LYS A 108 -1 N ALA A 102 O ASN A 215 SHEET 6 AA1 6 GLU A 64 SER A 67 -1 N GLU A 64 O VAL A 107 SHEET 1 AA2 4 ILE A 116 HIS A 119 0 SHEET 2 AA2 4 HIS A 198 SER A 200 -1 O HIS A 198 N HIS A 119 SHEET 3 AA2 4 LEU A 149 ILE A 152 -1 N GLU A 150 O HIS A 199 SHEET 4 AA2 4 ILE A 179 LEU A 180 -1 O LEU A 180 N TYR A 151 SHEET 1 AA3 2 VAL A 127 GLN A 128 0 SHEET 2 AA3 2 THR A 222 TYR A 223 -1 O THR A 222 N GLN A 128 LINK NE2 HIS A 119 FE FE A 302 1555 1555 2.29 LINK OD1 ASP A 121 FE FE A 302 1555 1555 2.32 LINK NE2 HIS A 198 FE FE A 302 1555 1555 2.24 LINK O2 AKG A 301 FE FE A 302 1555 1555 1.96 LINK O5 AKG A 301 FE FE A 302 1555 1555 2.18 LINK FE FE A 302 O HOH A 481 1555 1555 2.02 CISPEP 1 TRP A 230 PRO A 231 0 5.62 CRYST1 44.495 44.495 107.316 90.00 90.00 120.00 P 31 3 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 0.022474 0.012976 0.000000 0.00000 SCALE2 0.000000 0.025951 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009318 0.00000 CONECT 810 2038 CONECT 825 2038 CONECT 1478 2038 CONECT 2028 2029 2030 2031 CONECT 2029 2028 CONECT 2030 2028 2038 CONECT 2031 2028 2032 2033 CONECT 2032 2031 2038 CONECT 2033 2031 2034 CONECT 2034 2033 2035 CONECT 2035 2034 2036 2037 CONECT 2036 2035 CONECT 2037 2035 CONECT 2038 810 825 1478 2030 CONECT 2038 2032 2123 CONECT 2039 2040 2041 CONECT 2040 2039 CONECT 2041 2039 2042 CONECT 2042 2041 CONECT 2123 2038 MASTER 262 0 3 12 12 0 0 6 2260 1 20 21 END