HEADER OXIDOREDUCTASE 05-SEP-17 5YBO TITLE FE(II)/(ALPHA)KETOGLUTARATE-DEPENDENT DIOXYGENASE PRHA IN COMPLEX WITH TITLE 2 PREAUSTINOID A1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PRHA; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 6-294; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PENICILLIUM BRASILIANUM; SOURCE 3 ORGANISM_TAXID: 104259; SOURCE 4 GENE: PRHA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ALPHA-KEGOGLUTARATE-DEPENDENT DIOXYGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.NAKASHIMA,M.SENDA REVDAT 2 22-NOV-23 5YBO 1 LINK REVDAT 1 24-JAN-18 5YBO 0 JRNL AUTH Y.NAKASHIMA,T.MORI,H.NAKAMURA,T.AWAKAWA,S.HOSHINO,M.SENDA, JRNL AUTH 2 T.SENDA,I.ABE JRNL TITL STRUCTURE FUNCTION AND ENGINEERING OF MULTIFUNCTIONAL JRNL TITL 2 NON-HEME IRON DEPENDENT OXYGENASES IN FUNGAL MEROTERPENOID JRNL TITL 3 BIOSYNTHESIS. JRNL REF NAT COMMUN V. 9 104 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 29317628 JRNL DOI 10.1038/S41467-017-02371-W REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 39248 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.215 REMARK 3 R VALUE (WORKING SET) : 0.213 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.140 REMARK 3 FREE R VALUE TEST SET COUNT : 2018 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 40.3291 - 5.3101 0.94 2779 149 0.2056 0.2502 REMARK 3 2 5.3101 - 4.2163 0.94 2681 147 0.1652 0.2301 REMARK 3 3 4.2163 - 3.6837 0.94 2670 144 0.1701 0.2296 REMARK 3 4 3.6837 - 3.3471 0.94 2664 143 0.1883 0.2577 REMARK 3 5 3.3471 - 3.1073 0.95 2666 146 0.2126 0.2195 REMARK 3 6 3.1073 - 2.9241 0.94 2656 145 0.2230 0.2621 REMARK 3 7 2.9241 - 2.7777 0.94 2624 141 0.2422 0.2963 REMARK 3 8 2.7777 - 2.6568 0.95 2663 144 0.2617 0.2833 REMARK 3 9 2.6568 - 2.5546 0.95 2629 142 0.2631 0.2969 REMARK 3 10 2.5546 - 2.4664 0.95 2653 144 0.2720 0.3756 REMARK 3 11 2.4664 - 2.3893 0.95 2610 141 0.2699 0.3464 REMARK 3 12 2.3893 - 2.3210 0.95 2661 141 0.2971 0.3049 REMARK 3 13 2.3210 - 2.2599 0.95 2618 137 0.3208 0.3745 REMARK 3 14 2.2599 - 2.2048 0.94 2636 144 0.3249 0.3639 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 4441 REMARK 3 ANGLE : 0.938 6054 REMARK 3 CHIRALITY : 0.054 652 REMARK 3 PLANARITY : 0.008 814 REMARK 3 DIHEDRAL : 18.274 2626 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 5YBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-SEP-17. REMARK 100 THE DEPOSITION ID IS D_1300003501. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-16 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : BL17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39248 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 44.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX (1.10.1_2155) REMARK 200 STARTING MODEL: 5YBM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, LITHIUM CITRATE, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 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 30.44333 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 15.22167 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.44333 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 15.22167 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5060 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -50.0 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 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 -15 REMARK 465 GLY A -14 REMARK 465 SER A -13 REMARK 465 SER A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 SER A -5 REMARK 465 SER A -4 REMARK 465 GLY A -3 REMARK 465 ARG A 1 REMARK 465 GLY A 64 REMARK 465 ASN A 65 REMARK 465 ASP A 274 REMARK 465 SER A 296 REMARK 465 SER A 297 REMARK 465 ALA A 298 REMARK 465 MET B -15 REMARK 465 GLY B -14 REMARK 465 SER B -13 REMARK 465 SER B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 SER B -5 REMARK 465 SER B -4 REMARK 465 ALA B 14 REMARK 465 THR B 15 REMARK 465 ILE B 199 REMARK 465 ASN B 219 REMARK 465 ALA B 220 REMARK 465 SER B 269 REMARK 465 VAL B 270 REMARK 465 GLN B 271 REMARK 465 HIS B 272 REMARK 465 CYS B 273 REMARK 465 ASP B 274 REMARK 465 VAL B 275 REMARK 465 ASP B 276 REMARK 465 MET B 277 REMARK 465 VAL B 278 REMARK 465 SER B 297 REMARK 465 ALA B 298 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A -2 CG CD1 CD2 REMARK 470 VAL A -1 CG1 CG2 REMARK 470 MET A 5 CG SD CE REMARK 470 ARG A 11 NH1 NH2 REMARK 470 GLU A 20 CG CD OE1 OE2 REMARK 470 GLU A 40 CG CD OE1 OE2 REMARK 470 VAL A 42 CG1 CG2 REMARK 470 GLU A 54 CG CD OE1 OE2 REMARK 470 LYS A 55 CG CD CE NZ REMARK 470 ARG A 128 CG CD NE CZ NH1 NH2 REMARK 470 CYS A 149 SG REMARK 470 ASN A 152 CG OD1 ND2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 GLU A 178 CG CD OE1 OE2 REMARK 470 ARG A 185 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 192 CG CD CE NZ REMARK 470 ARG A 225 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 251 CG CD CE NZ REMARK 470 MET A 277 CG SD CE REMARK 470 VAL A 278 CG1 CG2 REMARK 470 LYS A 286 CG CD CE NZ REMARK 470 ILE A 295 CG1 CG2 CD1 REMARK 470 LEU B -2 CG CD1 CD2 REMARK 470 VAL B -1 CG1 CG2 REMARK 470 ARG B 1 CG CD NE CZ NH1 NH2 REMARK 470 MET B 5 CG SD CE REMARK 470 ARG B 8 CG CD NE CZ NH1 NH2 REMARK 470 SER B 17 OG REMARK 470 ASP B 19 CG OD1 OD2 REMARK 470 GLU B 20 CG CD OE1 OE2 REMARK 470 GLU B 27 CD OE1 OE2 REMARK 470 ASP B 28 OD1 OD2 REMARK 470 CYS B 30 SG REMARK 470 VAL B 32 CG1 CG2 REMARK 470 ILE B 33 CG1 CG2 CD1 REMARK 470 GLU B 34 CG CD OE1 OE2 REMARK 470 PHE B 36 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE B 37 CG1 CG2 CD1 REMARK 470 SER B 38 OG REMARK 470 GLU B 40 CG CD OE1 OE2 REMARK 470 VAL B 42 CG1 CG2 REMARK 470 ARG B 44 CG CD NE CZ NH1 NH2 REMARK 470 PHE B 45 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLN B 47 CG CD OE1 NE2 REMARK 470 ASP B 50 CG OD1 OD2 REMARK 470 GLU B 54 CG CD OE1 OE2 REMARK 470 LYS B 55 CG CD CE NZ REMARK 470 GLU B 59 CG CD OE1 OE2 REMARK 470 THR B 61 OG1 CG2 REMARK 470 ARG B 69 NH1 NH2 REMARK 470 ILE B 78 CG1 CG2 CD1 REMARK 470 ILE B 88 CG1 CG2 CD1 REMARK 470 GLU B 89 CG CD OE1 OE2 REMARK 470 SER B 90 OG REMARK 470 ASP B 91 CG OD1 OD2 REMARK 470 LEU B 92 CG CD1 CD2 REMARK 470 GLU B 95 CG CD OE1 OE2 REMARK 470 ASP B 98 CG OD1 OD2 REMARK 470 ARG B 99 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 103 CG CD CE NZ REMARK 470 VAL B 120 CG1 CG2 REMARK 470 GLN B 121 CG CD OE1 NE2 REMARK 470 PRO B 122 CG CD REMARK 470 VAL B 157 CG1 CG2 REMARK 470 PHE B 160 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 162 CG CD OE1 OE2 REMARK 470 GLU B 163 CG CD OE1 OE2 REMARK 470 ARG B 168 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 178 CG CD OE1 OE2 REMARK 470 ASN B 183 CG OD1 ND2 REMARK 470 GLU B 184 CG CD OE1 OE2 REMARK 470 ARG B 185 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 192 CG CD CE NZ REMARK 470 ILE B 193 CG1 CG2 CD1 REMARK 470 GLN B 201 CG CD OE1 NE2 REMARK 470 CYS B 205 SG REMARK 470 LEU B 207 CG CD1 CD2 REMARK 470 HIS B 218 CG ND1 CD2 CE1 NE2 REMARK 470 THR B 222 OG1 CG2 REMARK 470 THR B 223 OG1 CG2 REMARK 470 ARG B 225 CZ NH1 NH2 REMARK 470 ARG B 236 CZ NH1 NH2 REMARK 470 LYS B 251 CG CD CE NZ REMARK 470 HIS B 279 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 286 CG CD CE NZ REMARK 470 SER B 296 OG 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 O HOH A 487 O HOH B 473 2.06 REMARK 500 O HOH A 507 O HOH B 456 2.14 REMARK 500 O HOH A 435 O HOH A 485 2.18 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 ASN A 62 51.91 -94.20 REMARK 500 LYS A 75 47.56 -94.90 REMARK 500 GLU A 86 -53.48 -128.61 REMARK 500 VAL B 60 76.95 -103.40 REMARK 500 ASP B 68 99.52 -60.40 REMARK 500 LYS B 75 47.77 -77.22 REMARK 500 GLU B 86 -58.46 -125.08 REMARK 500 ILE B 88 0.73 -63.52 REMARK 500 LEU B 231 77.65 -105.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH B 475 DISTANCE = 5.91 ANGSTROMS 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 130 NE2 REMARK 620 2 ASP A 132 OD1 95.3 REMARK 620 3 HIS A 214 NE2 92.6 90.1 REMARK 620 4 AKG A 302 O2 89.2 96.3 173.2 REMARK 620 5 AKG A 302 O5 98.9 165.5 86.5 86.7 REMARK 620 6 HOH A 408 O 176.8 87.9 87.7 90.0 77.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE B 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 130 NE2 REMARK 620 2 ASP B 132 OD1 100.9 REMARK 620 3 HIS B 214 NE2 83.7 82.2 REMARK 620 4 AKG B 302 O5 88.9 170.1 97.8 REMARK 620 5 AKG B 302 O2 101.6 102.0 172.5 77.0 REMARK 620 6 HOH B 421 O 164.0 75.2 80.4 95.0 94.5 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 FE A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 8SX B 303 DBREF1 5YBO A 6 294 UNP A0A1E1FFL0_9EURO DBREF2 5YBO A A0A1E1FFL0 6 294 DBREF1 5YBO B 6 294 UNP A0A1E1FFL0_9EURO DBREF2 5YBO B A0A1E1FFL0 6 294 SEQADV 5YBO MET A -15 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO GLY A -14 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER A -13 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER A -12 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS A -11 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS A -10 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS A -9 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS A -8 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS A -7 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS A -6 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER A -5 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER A -4 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO GLY A -3 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO LEU A -2 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO VAL A -1 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO PRO A 0 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO ARG A 1 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO GLY A 2 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER A 3 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS A 4 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO MET A 5 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO ILE A 295 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER A 296 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER A 297 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO ALA A 298 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO MET B -15 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO GLY B -14 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER B -13 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER B -12 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS B -11 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS B -10 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS B -9 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS B -8 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS B -7 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS B -6 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER B -5 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER B -4 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO GLY B -3 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO LEU B -2 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO VAL B -1 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO PRO B 0 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO ARG B 1 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO GLY B 2 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER B 3 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO HIS B 4 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO MET B 5 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO ILE B 295 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER B 296 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO SER B 297 UNP A0A1E1FFL EXPRESSION TAG SEQADV 5YBO ALA B 298 UNP A0A1E1FFL EXPRESSION TAG SEQRES 1 A 314 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 314 LEU VAL PRO ARG GLY SER HIS MET PRO PRO ARG LEU GLN SEQRES 3 A 314 ARG PHE PRO ALA THR ALA SER ALA ASP GLU ILE PHE ALA SEQRES 4 A 314 ALA PHE GLN GLU ASP GLY CYS VAL VAL ILE GLU GLY PHE SEQRES 5 A 314 ILE SER PRO GLU GLN VAL ALA ARG PHE SER GLN GLU VAL SEQRES 6 A 314 ASP PRO ALA MET GLU LYS ILE PRO VAL GLU VAL THR ASN SEQRES 7 A 314 ASN GLY ASN SER ASN ASP ARG THR LYS ARG PHE SER LYS SEQRES 8 A 314 CYS VAL ILE ALA SER PRO THR PHE ARG ASN GLU ILE ILE SEQRES 9 A 314 GLU SER ASP LEU MET HIS GLU LEU CYS ASP ARG VAL PHE SEQRES 10 A 314 SER LYS PRO GLY GLU GLY MET GLY TYR HIS PHE ASN ASP SEQRES 11 A 314 ASN MET VAL ILE GLU VAL GLN PRO GLY ALA PRO ALA GLN SEQRES 12 A 314 ARG LEU HIS ARG ASP GLN GLU LEU TYR PRO TRP TRP ASN SEQRES 13 A 314 SER MET GLY PRO ALA GLY PRO GLU CYS VAL ILE ASN PHE SEQRES 14 A 314 PHE CYS ALA VAL THR PRO PHE THR GLU GLU ASN GLY ALA SEQRES 15 A 314 THR ARG LEU VAL PRO GLY SER HIS LEU TRP PRO GLU PHE SEQRES 16 A 314 THR GLN ILE ASN GLU ARG ASP CYS PRO GLN PHE GLY LYS SEQRES 17 A 314 ILE GLU THR VAL PRO ALA ILE MET GLN PRO GLY ASP CYS SEQRES 18 A 314 TYR LEU MET SER GLY LYS VAL ILE HIS GLY ALA GLY HIS SEQRES 19 A 314 ASN ALA THR THR THR ASP ARG ARG ARG ALA LEU ALA LEU SEQRES 20 A 314 ALA ILE ILE ARG ARG GLU LEU ARG PRO MET GLN ALA PHE SEQRES 21 A 314 SER LEU SER VAL PRO MET LYS LEU ALA ARG GLU MET SER SEQRES 22 A 314 GLU ARG SER GLN THR MET PHE GLY PHE ARG SER SER VAL SEQRES 23 A 314 GLN HIS CYS ASP VAL ASP MET VAL HIS PHE TRP GLY ASN SEQRES 24 A 314 ASP GLY LYS ASP ILE ALA HIS HIS LEU GLY LEU ILE SER SEQRES 25 A 314 SER ALA SEQRES 1 B 314 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 314 LEU VAL PRO ARG GLY SER HIS MET PRO PRO ARG LEU GLN SEQRES 3 B 314 ARG PHE PRO ALA THR ALA SER ALA ASP GLU ILE PHE ALA SEQRES 4 B 314 ALA PHE GLN GLU ASP GLY CYS VAL VAL ILE GLU GLY PHE SEQRES 5 B 314 ILE SER PRO GLU GLN VAL ALA ARG PHE SER GLN GLU VAL SEQRES 6 B 314 ASP PRO ALA MET GLU LYS ILE PRO VAL GLU VAL THR ASN SEQRES 7 B 314 ASN GLY ASN SER ASN ASP ARG THR LYS ARG PHE SER LYS SEQRES 8 B 314 CYS VAL ILE ALA SER PRO THR PHE ARG ASN GLU ILE ILE SEQRES 9 B 314 GLU SER ASP LEU MET HIS GLU LEU CYS ASP ARG VAL PHE SEQRES 10 B 314 SER LYS PRO GLY GLU GLY MET GLY TYR HIS PHE ASN ASP SEQRES 11 B 314 ASN MET VAL ILE GLU VAL GLN PRO GLY ALA PRO ALA GLN SEQRES 12 B 314 ARG LEU HIS ARG ASP GLN GLU LEU TYR PRO TRP TRP ASN SEQRES 13 B 314 SER MET GLY PRO ALA GLY PRO GLU CYS VAL ILE ASN PHE SEQRES 14 B 314 PHE CYS ALA VAL THR PRO PHE THR GLU GLU ASN GLY ALA SEQRES 15 B 314 THR ARG LEU VAL PRO GLY SER HIS LEU TRP PRO GLU PHE SEQRES 16 B 314 THR GLN ILE ASN GLU ARG ASP CYS PRO GLN PHE GLY LYS SEQRES 17 B 314 ILE GLU THR VAL PRO ALA ILE MET GLN PRO GLY ASP CYS SEQRES 18 B 314 TYR LEU MET SER GLY LYS VAL ILE HIS GLY ALA GLY HIS SEQRES 19 B 314 ASN ALA THR THR THR ASP ARG ARG ARG ALA LEU ALA LEU SEQRES 20 B 314 ALA ILE ILE ARG ARG GLU LEU ARG PRO MET GLN ALA PHE SEQRES 21 B 314 SER LEU SER VAL PRO MET LYS LEU ALA ARG GLU MET SER SEQRES 22 B 314 GLU ARG SER GLN THR MET PHE GLY PHE ARG SER SER VAL SEQRES 23 B 314 GLN HIS CYS ASP VAL ASP MET VAL HIS PHE TRP GLY ASN SEQRES 24 B 314 ASP GLY LYS ASP ILE ALA HIS HIS LEU GLY LEU ILE SER SEQRES 25 B 314 SER ALA HET FE A 301 1 HET AKG A 302 10 HET FE B 301 1 HET AKG B 302 10 HET 8SX B 303 33 HETNAM FE FE (III) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM 8SX PREAUSTINOID A1 FORMUL 3 FE 2(FE 3+) FORMUL 4 AKG 2(C5 H6 O5) FORMUL 7 8SX C26 H36 O7 FORMUL 8 HOH *183(H2 O) HELIX 1 AA1 SER A 17 GLY A 29 1 13 HELIX 2 AA2 SER A 38 LYS A 55 1 18 HELIX 3 AA3 LYS A 75 SER A 80 1 6 HELIX 4 AA4 SER A 80 GLU A 86 1 7 HELIX 5 AA5 ILE A 87 GLU A 89 5 3 HELIX 6 AA6 SER A 90 SER A 102 1 13 HELIX 7 AA7 ARG A 131 TYR A 136 5 6 HELIX 8 AA8 TRP A 138 GLY A 146 5 9 HELIX 9 AA9 GLY A 172 TRP A 176 5 5 HELIX 10 AB1 ALA A 243 VAL A 248 1 6 HELIX 11 AB2 PRO A 249 GLU A 255 1 7 HELIX 12 AB3 SER A 257 PHE A 264 1 8 HELIX 13 AB4 ASP A 287 GLY A 293 1 7 HELIX 14 AB5 SER B 17 GLY B 29 1 13 HELIX 15 AB6 SER B 38 LYS B 55 1 18 HELIX 16 AB7 LYS B 75 SER B 80 1 6 HELIX 17 AB8 SER B 80 GLU B 86 1 7 HELIX 18 AB9 ILE B 87 GLU B 89 5 3 HELIX 19 AC1 SER B 90 PHE B 101 1 12 HELIX 20 AC2 GLN B 133 TYR B 136 5 4 HELIX 21 AC3 TRP B 138 GLY B 146 5 9 HELIX 22 AC4 ALA B 243 VAL B 248 1 6 HELIX 23 AC5 PRO B 249 GLU B 255 1 7 HELIX 24 AC6 SER B 257 PHE B 264 1 8 HELIX 25 AC7 ASP B 287 LEU B 292 1 6 SHEET 1 AA1 7 ARG A 11 PRO A 13 0 SHEET 2 AA1 7 CYS A 30 GLU A 34 1 O GLU A 34 N PHE A 12 SHEET 3 AA1 7 CYS A 205 SER A 209 -1 O CYS A 205 N ILE A 33 SHEET 4 AA1 7 VAL A 150 ALA A 156 -1 N PHE A 154 O TYR A 206 SHEET 5 AA1 7 ARG A 226 ARG A 235 -1 O ILE A 233 N ILE A 151 SHEET 6 AA1 7 TYR A 110 VAL A 120 -1 N MET A 116 O ALA A 230 SHEET 7 AA1 7 THR A 70 PHE A 73 -1 N PHE A 73 O VAL A 117 SHEET 1 AA2 3 VAL A 196 PRO A 197 0 SHEET 2 AA2 3 ARG A 168 VAL A 170 -1 N LEU A 169 O VAL A 196 SHEET 3 AA2 3 ILE A 213 GLY A 215 -1 O GLY A 215 N ARG A 168 SHEET 1 AA3 2 SER A 269 HIS A 272 0 SHEET 2 AA3 2 MET A 277 PHE A 280 -1 O VAL A 278 N GLN A 271 SHEET 1 AA4 7 ARG B 11 PHE B 12 0 SHEET 2 AA4 7 CYS B 30 ILE B 33 1 O VAL B 32 N PHE B 12 SHEET 3 AA4 7 CYS B 205 SER B 209 -1 O CYS B 205 N ILE B 33 SHEET 4 AA4 7 VAL B 150 ALA B 156 -1 N PHE B 154 O TYR B 206 SHEET 5 AA4 7 ARG B 226 ARG B 235 -1 O ILE B 233 N ILE B 151 SHEET 6 AA4 7 TYR B 110 VAL B 120 -1 N MET B 116 O ALA B 230 SHEET 7 AA4 7 THR B 70 PHE B 73 -1 N LYS B 71 O GLU B 119 SHEET 1 AA5 4 HIS B 130 ARG B 131 0 SHEET 2 AA5 4 ILE B 213 ALA B 216 -1 O HIS B 214 N HIS B 130 SHEET 3 AA5 4 THR B 167 VAL B 170 -1 N ARG B 168 O GLY B 215 SHEET 4 AA5 4 VAL B 196 PRO B 197 -1 O VAL B 196 N LEU B 169 LINK NE2 HIS A 130 FE FE A 301 1555 1555 2.36 LINK OD1 ASP A 132 FE FE A 301 1555 1555 2.14 LINK NE2 HIS A 214 FE FE A 301 1555 1555 2.06 LINK FE FE A 301 O2 AKG A 302 1555 1555 1.78 LINK FE FE A 301 O5 AKG A 302 1555 1555 2.21 LINK FE FE A 301 O HOH A 408 1555 1555 2.26 LINK NE2 HIS B 130 FE FE B 301 1555 1555 2.23 LINK OD1 ASP B 132 FE FE B 301 1555 1555 2.43 LINK NE2 HIS B 214 FE FE B 301 1555 1555 2.24 LINK FE FE B 301 O5 AKG B 302 1555 1555 2.35 LINK FE FE B 301 O2 AKG B 302 1555 1555 2.27 LINK FE FE B 301 O HOH B 421 1555 1555 1.91 SITE 1 AC1 5 HIS A 130 ASP A 132 HIS A 214 AKG A 302 SITE 2 AC1 5 HOH A 408 SITE 1 AC2 11 GLN A 127 HIS A 130 ASP A 132 PHE A 154 SITE 2 AC2 11 THR A 167 HIS A 214 ALA A 216 ARG A 226 SITE 3 AC2 11 FE A 301 HOH A 408 HOH A 429 SITE 1 AC3 5 HIS B 130 ASP B 132 HIS B 214 AKG B 302 SITE 2 AC3 5 HOH B 421 SITE 1 AC4 13 ARG B 72 ILE B 118 GLN B 127 HIS B 130 SITE 2 AC4 13 ASP B 132 PHE B 154 THR B 167 HIS B 214 SITE 3 AC4 13 ALA B 216 ARG B 226 FE B 301 8SX B 303 SITE 4 AC4 13 HOH B 421 SITE 1 AC5 17 ASP A 276 MET A 277 VAL A 278 SER B 66 SITE 2 AC5 17 ASN B 67 ARG B 72 ASN B 113 MET B 116 SITE 3 AC5 17 GLN B 127 ARG B 128 HIS B 130 ASP B 132 SITE 4 AC5 17 VAL B 150 ASN B 152 ALA B 232 MET B 241 SITE 5 AC5 17 AKG B 302 CRYST1 171.816 171.816 45.665 90.00 90.00 120.00 P 62 12 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 0.005820 0.003360 0.000000 0.00000 SCALE2 0.000000 0.006721 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021899 0.00000