HEADER OXIDOREDUCTASE 20-JUN-17 5O9W TITLE THEBAINE 6-O-DEMETHYLASE (T6ODM) FROM PAPAVER SOMNIFERUM IN COMPLEX TITLE 2 WITH 2-OXOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THEBAINE 6-O-DEMETHYLASE; COMPND 3 CHAIN: A; COMPND 4 EC: 1.14.11.31; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAPAVER SOMNIFERUM; SOURCE 3 ORGANISM_COMMON: OPIUM POPPY; SOURCE 4 ORGANISM_TAXID: 3469; SOURCE 5 GENE: T6ODM, DIOX1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: MAGIC; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMCSG19 KEYWDS 2-OXOGLUTARATE DEPENDENT DIOXYGENASE, MORPHINE BIOSYNTHESIS, KEYWDS 2 ORIPAVINE, THEBAINE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KLUZA,E.NIEDZIALKOWSKA,K.KURPIEWSKA,P.J.POREBSKI,T.BOROWSKI REVDAT 5 17-JAN-24 5O9W 1 LINK REVDAT 4 22-APR-20 5O9W 1 REMARK REVDAT 3 23-MAY-18 5O9W 1 JRNL REVDAT 2 04-APR-18 5O9W 1 REMARK REVDAT 1 14-FEB-18 5O9W 0 JRNL AUTH A.KLUZA,E.NIEDZIALKOWSKA,K.KURPIEWSKA,Z.WOJDYLA,M.QUESNE, JRNL AUTH 2 E.KOT,P.J.POREBSKI,T.BOROWSKI JRNL TITL CRYSTAL STRUCTURE OF THEBAINE 6-O-DEMETHYLASE FROM THE JRNL TITL 2 MORPHINE BIOSYNTHESIS PATHWAY. JRNL REF J. STRUCT. BIOL. V. 202 229 2018 JRNL REFN ESSN 1095-8657 JRNL PMID 29408320 JRNL DOI 10.1016/J.JSB.2018.01.007 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.43 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 31662 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 + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1633 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2103 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.28 REMARK 3 BIN R VALUE (WORKING SET) : 0.2230 REMARK 3 BIN FREE R VALUE SET COUNT : 97 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2766 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 77 REMARK 3 SOLVENT ATOMS : 377 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.61 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.29000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : 0.20000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.132 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.087 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.912 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3036 ; 0.010 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2920 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4097 ; 1.414 ; 1.996 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6822 ; 0.911 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 396 ; 6.283 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 123 ;35.451 ;25.366 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 559 ;12.019 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;16.878 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 464 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3309 ; 0.006 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 550 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1481 ; 1.799 ; 2.337 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1480 ; 1.796 ; 2.336 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1862 ; 3.017 ; 3.482 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1863 ; 3.018 ; 3.482 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1555 ; 1.813 ; 2.492 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1555 ; 1.809 ; 2.492 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2218 ; 2.820 ; 3.628 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3362 ; 5.429 ;27.658 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3363 ; 5.429 ;27.666 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5O9W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1200005428. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : 9.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : AGILENT SUPERNOVA REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : AGILENT ATLAS CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33795 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 41.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.400 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.7730 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.271 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: HKL-3000, MOLREP REMARK 200 STARTING MODEL: 5O7Y REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19% PEG 3350, 200 MM DISODIUM 2 REMARK 280 -OXOGLUTARATE. CONCENTRATION OF PROTEIN 37.5 MG/ML., PH 9.4, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 23.52200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 47.43150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.71200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.43150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.52200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.71200 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 TOTAL BURIED SURFACE AREA: 4310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 31.0 KCAL/MOL 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 ASN A 37 REMARK 465 GLU A 38 REMARK 465 ASN A 39 REMARK 465 LEU A 40 REMARK 465 ALA A 46 REMARK 465 SER A 47 REMARK 465 VAL A 48 REMARK 465 ILE A 49 REMARK 465 ASN A 50 REMARK 465 ASP A 51 REMARK 465 HIS A 52 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 GLU A 124 CG CD OE1 OE2 REMARK 470 GLN A 200 CG CD OE1 NE2 REMARK 470 LYS A 352 CG CD CE NZ REMARK 470 LEU A 353 CG CD1 CD2 REMARK 470 ASP A 354 CG OD1 OD2 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 635 O HOH A 777 1.91 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 GLU A 252 43.15 -94.21 REMARK 500 ASN A 272 52.26 -113.50 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 A 876 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 877 DISTANCE = 7.30 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 NI A 401 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 238 NE2 REMARK 620 2 ASP A 240 OD1 88.9 REMARK 620 3 HIS A 295 NE2 87.7 92.7 REMARK 620 4 AKG A 402 O1 94.8 97.0 170.0 REMARK 620 5 AKG A 402 O5 95.7 172.1 93.9 76.3 REMARK 620 6 HOH A 526 O 178.7 90.7 91.0 86.5 84.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 423 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 324 O REMARK 620 2 ILE A 327 O 90.3 REMARK 620 3 HOH A 603 O 166.3 76.0 REMARK 620 4 HOH A 802 O 89.4 158.9 103.8 REMARK 620 5 HOH A 813 O 104.0 94.0 78.7 65.6 REMARK 620 6 HOH A 818 O 95.9 116.5 89.1 84.5 143.4 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue AKG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 415 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UNX A 416 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UNX A 417 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UNX A 418 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UNX A 419 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UNX A 420 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue UNX A 421 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 422 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 423 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5O7Y RELATED DB: PDB REMARK 900 COMPLEX WITH SUCCINATE DBREF 5O9W A 1 364 UNP D4N500 DIOX1_PAPSO 1 364 SEQADV 5O9W SER A -2 UNP D4N500 EXPRESSION TAG SEQADV 5O9W ASN A -1 UNP D4N500 EXPRESSION TAG SEQADV 5O9W ALA A 0 UNP D4N500 EXPRESSION TAG SEQRES 1 A 367 SER ASN ALA MET GLU LYS ALA LYS LEU MET LYS LEU GLY SEQRES 2 A 367 ASN GLY MET GLU ILE PRO SER VAL GLN GLU LEU ALA LYS SEQRES 3 A 367 LEU THR LEU ALA GLU ILE PRO SER ARG TYR VAL CYS ALA SEQRES 4 A 367 ASN GLU ASN LEU LEU LEU PRO MET GLY ALA SER VAL ILE SEQRES 5 A 367 ASN ASP HIS GLU THR ILE PRO VAL ILE ASP ILE GLU ASN SEQRES 6 A 367 LEU LEU SER PRO GLU PRO ILE ILE GLY LYS LEU GLU LEU SEQRES 7 A 367 ASP ARG LEU HIS PHE ALA CYS LYS GLU TRP GLY PHE PHE SEQRES 8 A 367 GLN VAL VAL ASN HIS GLY VAL ASP ALA SER LEU VAL ASP SEQRES 9 A 367 SER VAL LYS SER GLU ILE GLN GLY PHE PHE ASN LEU SER SEQRES 10 A 367 MET ASP GLU LYS THR LYS TYR GLU GLN GLU ASP GLY ASP SEQRES 11 A 367 VAL GLU GLY PHE GLY GLN GLY PHE ILE GLU SER GLU ASP SEQRES 12 A 367 GLN THR LEU ASP TRP ALA ASP ILE PHE MET MET PHE THR SEQRES 13 A 367 LEU PRO LEU HIS LEU ARG LYS PRO HIS LEU PHE SER LYS SEQRES 14 A 367 LEU PRO VAL PRO LEU ARG GLU THR ILE GLU SER TYR SER SEQRES 15 A 367 SER GLU MET LYS LYS LEU SER MET VAL LEU PHE ASN LYS SEQRES 16 A 367 MET GLU LYS ALA LEU GLN VAL GLN ALA ALA GLU ILE LYS SEQRES 17 A 367 GLY MET SER GLU VAL PHE ILE ASP GLY THR GLN ALA MET SEQRES 18 A 367 ARG MET ASN TYR TYR PRO PRO CYS PRO GLN PRO ASN LEU SEQRES 19 A 367 ALA ILE GLY LEU THR SER HIS SER ASP PHE GLY GLY LEU SEQRES 20 A 367 THR ILE LEU LEU GLN ILE ASN GLU VAL GLU GLY LEU GLN SEQRES 21 A 367 ILE LYS ARG GLU GLY THR TRP ILE SER VAL LYS PRO LEU SEQRES 22 A 367 PRO ASN ALA PHE VAL VAL ASN VAL GLY ASP ILE LEU GLU SEQRES 23 A 367 ILE MET THR ASN GLY ILE TYR HIS SER VAL ASP HIS ARG SEQRES 24 A 367 ALA VAL VAL ASN SER THR ASN GLU ARG LEU SER ILE ALA SEQRES 25 A 367 THR PHE HIS ASP PRO SER LEU GLU SER VAL ILE GLY PRO SEQRES 26 A 367 ILE SER SER LEU ILE THR PRO GLU THR PRO ALA LEU PHE SEQRES 27 A 367 LYS SER GLY SER THR TYR GLY ASP LEU VAL GLU GLU CYS SEQRES 28 A 367 LYS THR ARG LYS LEU ASP GLY LYS SER PHE LEU ASP SER SEQRES 29 A 367 MET ARG ILE HET NI A 401 1 HET AKG A 402 10 HET EDO A 403 4 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET EDO A 410 4 HET EDO A 411 4 HET EDO A 412 4 HET EDO A 413 4 HET EDO A 414 4 HET EDO A 415 4 HET UNX A 416 1 HET UNX A 417 1 HET UNX A 418 1 HET UNX A 419 1 HET UNX A 420 1 HET UNX A 421 1 HET PEG A 422 7 HET NA A 423 1 HETNAM NI NICKEL (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM EDO 1,2-ETHANEDIOL HETNAM UNX UNKNOWN ATOM OR ION HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NI NI 2+ FORMUL 3 AKG C5 H6 O5 FORMUL 4 EDO 13(C2 H6 O2) FORMUL 17 UNX 6(X) FORMUL 23 PEG C4 H10 O3 FORMUL 24 NA NA 1+ FORMUL 25 HOH *377(H2 O) HELIX 1 AA1 ASN A -1 LYS A 8 1 10 HELIX 2 AA2 SER A 17 LYS A 23 1 7 HELIX 3 AA3 PRO A 30 VAL A 34 5 5 HELIX 4 AA4 ILE A 60 LEU A 64 1 5 HELIX 5 AA5 GLU A 67 TRP A 85 1 19 HELIX 6 AA6 ASP A 96 ASN A 112 1 17 HELIX 7 AA7 SER A 114 THR A 119 1 6 HELIX 8 AA8 PRO A 155 ARG A 159 5 5 HELIX 9 AA9 LYS A 160 LEU A 167 1 8 HELIX 10 AB1 PRO A 168 LEU A 197 1 30 HELIX 11 AB2 MET A 207 ILE A 212 1 6 HELIX 12 AB3 GLY A 279 THR A 286 1 8 HELIX 13 AB4 ILE A 323 ILE A 327 5 5 HELIX 14 AB5 TYR A 341 THR A 350 1 10 HELIX 15 AB6 SER A 357 MET A 362 1 6 SHEET 1 AA1 8 VAL A 57 ASP A 59 0 SHEET 2 AA1 8 PHE A 87 VAL A 91 1 O GLN A 89 N ILE A 58 SHEET 3 AA1 8 PHE A 274 VAL A 278 -1 O VAL A 276 N PHE A 88 SHEET 4 AA1 8 LEU A 244 GLN A 249 -1 N LEU A 247 O VAL A 275 SHEET 5 AA1 8 ARG A 305 ASP A 313 -1 O ILE A 308 N LEU A 248 SHEET 6 AA1 8 THR A 215 TYR A 223 -1 N ASN A 221 O SER A 307 SHEET 7 AA1 8 ASP A 147 LEU A 154 -1 N PHE A 149 O MET A 220 SHEET 8 AA1 8 GLY A 130 PHE A 131 -1 N GLY A 130 O MET A 150 SHEET 1 AA2 4 LEU A 235 HIS A 238 0 SHEET 2 AA2 4 HIS A 295 ALA A 297 -1 O HIS A 295 N HIS A 238 SHEET 3 AA2 4 LEU A 256 ARG A 260 -1 N GLN A 257 O ARG A 296 SHEET 4 AA2 4 THR A 263 SER A 266 -1 O THR A 263 N ARG A 260 SHEET 1 AA3 2 VAL A 319 ILE A 320 0 SHEET 2 AA3 2 SER A 339 THR A 340 -1 O SER A 339 N ILE A 320 LINK NE2 HIS A 238 NI NI A 401 1555 1555 2.14 LINK OD1 ASP A 240 NI NI A 401 1555 1555 2.19 LINK NE2 HIS A 295 NI NI A 401 1555 1555 2.12 LINK O SER A 324 NA NA A 423 1555 1555 2.39 LINK O ILE A 327 NA NA A 423 1555 1555 2.39 LINK NI NI A 401 O1 AKG A 402 1555 1555 2.06 LINK NI NI A 401 O5 AKG A 402 1555 1555 2.21 LINK NI NI A 401 O HOH A 526 1555 1555 2.10 LINK NA NA A 423 O HOH A 603 1555 4565 2.39 LINK NA NA A 423 O HOH A 802 1555 1555 2.41 LINK NA NA A 423 O HOH A 813 1555 1555 2.38 LINK NA NA A 423 O HOH A 818 1555 1555 2.37 CISPEP 1 LEU A 154 PRO A 155 0 -8.25 SITE 1 AC1 5 HIS A 238 ASP A 240 HIS A 295 AKG A 402 SITE 2 AC1 5 HOH A 526 SITE 1 AC2 16 ARG A 219 ASN A 221 TYR A 223 LEU A 235 SITE 2 AC2 16 HIS A 238 ASP A 240 LEU A 247 LEU A 256 SITE 3 AC2 16 HIS A 295 ARG A 305 SER A 307 ALA A 309 SITE 4 AC2 16 PHE A 311 NI A 401 HOH A 526 HOH A 702 SITE 1 AC3 4 LYS A 72 LEU A 75 ASP A 76 HIS A 79 SITE 1 AC4 5 PRO A 56 VAL A 57 ARG A 77 HOH A 618 SITE 2 AC4 5 HOH A 660 SITE 1 AC5 8 ILE A 284 ILE A 320 GLY A 321 LYS A 336 SITE 2 AC5 8 SER A 337 GLY A 338 SER A 339 MET A 362 SITE 1 AC6 1 HOH A 715 SITE 1 AC7 5 ASP A 76 ARG A 77 HOH A 513 HOH A 609 SITE 2 AC7 5 HOH A 697 SITE 1 AC8 8 GLN A 123 GLY A 132 GLN A 133 GLY A 134 SITE 2 AC8 8 PHE A 135 HOH A 598 HOH A 612 HOH A 717 SITE 1 AC9 2 GLY A 94 HOH A 633 SITE 1 AD1 7 GLU A 117 LYS A 118 LYS A 120 TYR A 121 SITE 2 AD1 7 LYS A 166 HOH A 617 HOH A 647 SITE 1 AD2 7 LYS A 205 GLY A 206 VAL A 210 VAL A 319 SITE 2 AD2 7 ILE A 320 GLY A 321 ILE A 323 SITE 1 AD3 4 HIS A 93 GLU A 181 LYS A 184 HOH A 540 SITE 1 AD4 5 ASN A 11 ASP A 59 VAL A 91 HOH A 541 SITE 2 AD4 5 HOH A 692 SITE 1 AD5 1 ILE A 69 SITE 1 AD6 3 ALA A 22 LYS A 23 HOH A 587 SITE 1 AD7 4 SER A -2 ASN A -1 ALA A 0 UNX A 417 SITE 1 AD8 3 LYS A 3 UNX A 416 UNX A 418 SITE 1 AD9 2 LYS A 3 UNX A 417 SITE 1 AE1 3 LYS A 336 SER A 337 SER A 339 SITE 1 AE2 5 LYS A 336 GLU A 347 MET A 362 UNX A 421 SITE 2 AE2 5 HOH A 747 SITE 1 AE3 4 LYS A 336 SER A 339 GLU A 347 UNX A 420 SITE 1 AE4 5 VAL A 128 MET A 150 HOH A 508 HOH A 539 SITE 2 AE4 5 HOH A 636 SITE 1 AE5 6 SER A 324 ILE A 327 HOH A 603 HOH A 802 SITE 2 AE5 6 HOH A 813 HOH A 818 CRYST1 47.044 87.424 94.863 90.00 90.00 90.00 P 21 21 21 4 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 0.021257 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011439 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010542 0.00000