HEADER OXIDOREDUCTASE 11-OCT-17 5YJW TITLE STRUCTURE OF THE NDI1 PROTEIN FROM SACCHAROMYCES CEREVISIAE IN COMPLEX TITLE 2 WITH THE COMPETITIVE INHIBITOR, STIGMATELLIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ROTENONE-INSENSITIVE NADH-UBIQUINONE OXIDOREDUCTASE, COMPND 3 MITOCHONDRIAL; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 30-513; COMPND 6 SYNONYM: INTERNAL NADH DEHYDROGENASE,NADH:UBIQUINONE REDUCTASE (NON- COMPND 7 ELECTROGENIC); COMPND 8 EC: 1.6.5.9; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: NDI1, YML120C, YM7056.06C; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MONOTOPIC MEMBRANE PROTEIN, NUCLEOTIDE-BINDING DOMAIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.YAMASITA,D.K.INAOKA,T.SHIBA,T.OOHASHI,S.IWATA,T.YAGI,H.KOSAKA, AUTHOR 2 S.HARADA,K.KITA,K.HIRANO REVDAT 3 22-NOV-23 5YJW 1 LINK REVDAT 2 21-FEB-18 5YJW 1 JRNL REVDAT 1 14-FEB-18 5YJW 0 JRNL AUTH T.YAMASHITA,D.K.INAOKA,T.SHIBA,T.OOHASHI,S.IWATA,T.YAGI, JRNL AUTH 2 H.KOSAKA,H.MIYOSHI,S.HARADA,K.KITA,K.HIRANO JRNL TITL UBIQUINONE BINDING SITE OF YEAST NADH DEHYDROGENASE REVEALED JRNL TITL 2 BY STRUCTURES BINDING NOVEL COMPETITIVE- AND MIXED-TYPE JRNL TITL 3 INHIBITORS JRNL REF SCI REP V. 8 2427 2018 JRNL REFN ESSN 2045-2322 JRNL PMID 29402945 JRNL DOI 10.1038/S41598-018-20775-6 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.48 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 49008 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2632 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) : 1920 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 49.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 85 REMARK 3 BIN FREE R VALUE : 0.2170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3578 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 317 REMARK 3 SOLVENT ATOMS : 345 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.26 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.04000 REMARK 3 B33 (A**2) : 0.03000 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): 0.118 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.083 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.811 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.945 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4132 ; 0.007 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 4088 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5555 ; 1.443 ; 2.043 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9439 ; 1.121 ; 3.007 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 477 ; 5.626 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 161 ;32.089 ;24.037 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 676 ;13.426 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;15.500 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 600 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4409 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 890 ; 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): 1881 ; 0.914 ; 2.064 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1880 ; 0.914 ; 2.064 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2367 ; 1.626 ; 3.086 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2368 ; 1.626 ; 3.086 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2251 ; 1.043 ; 2.557 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2252 ; 1.043 ; 2.558 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3189 ; 1.789 ; 3.669 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4872 ; 5.671 ;19.170 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4748 ; 5.389 ;18.775 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 : MASK 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 5YJW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005417. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0-6.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.90000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49022 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.78600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 4G9K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50MM MES(PH 6.0), 34%(V/V) PEG 400, REMARK 280 100MM NACL, 2% (V/V) ETHYLENE GLYCOL, 5%(V/V) GLYCEROL, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.35550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.35550 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 1.000000 0.000000 0.000000 58.33500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 64.22800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 58.33500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 64.22800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.35550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 58.33500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 64.22800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.35550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 58.33500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 64.22800 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 17620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 43020 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 43.35550 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 805 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 992 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1038 LIES ON A SPECIAL POSITION. 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 VAL A 30 REMARK 465 GLU A 31 REMARK 465 ASN A 32 REMARK 465 GLN A 49 REMARK 465 HIS A 50 REMARK 465 VAL A 147 REMARK 465 SER A 148 REMARK 465 GLN A 149 REMARK 465 LEU A 150 REMARK 465 TYR A 151 REMARK 465 GLN A 152 REMARK 465 PRO A 153 REMARK 465 GLU A 154 REMARK 465 ASN A 155 REMARK 465 HIS A 156 REMARK 465 LEU A 157 REMARK 465 GLY A 158 REMARK 465 LEU A 159 REMARK 465 HIS A 160 REMARK 465 GLN A 161 REMARK 465 ALA A 162 REMARK 465 GLU A 163 REMARK 465 PRO A 164 REMARK 465 ASN A 419 REMARK 465 LEU A 420 REMARK 465 SER A 421 REMARK 465 SER A 422 REMARK 465 ARG A 423 REMARK 465 LYS A 424 REMARK 465 ASP A 425 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 61 40.77 -141.34 REMARK 500 LEU A 144 -50.49 -28.35 REMARK 500 ALA A 175 50.28 -143.77 REMARK 500 LYS A 196 -38.49 -139.50 REMARK 500 SER A 297 3.06 86.07 REMARK 500 LYS A 361 -63.09 -131.60 REMARK 500 SER A 461 105.78 -162.94 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 MG A 603 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 175 O REMARK 620 2 FAD A 601 O1P 96.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 381 O REMARK 620 2 FAD A 601 O2P 108.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 605 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 383 OD2 REMARK 620 2 FAD A 601 O2A 128.9 REMARK 620 3 HOH A 703 O 163.9 64.5 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 604 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 FAD A 601 O1A REMARK 620 2 FAD A 601 O2A 52.4 REMARK 620 3 HOH A 731 O 126.0 84.8 REMARK 620 4 HOH A 832 O 66.1 116.5 152.3 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 FAD A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PE4 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue P6G A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 613 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 614 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 615 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 616 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 617 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG A 618 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 619 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 620 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 621 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 622 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 623 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES A 624 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SMA A 625 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SMA A 626 DBREF 5YJW A 30 513 UNP P32340 NDI1_YEAST 30 513 SEQRES 1 A 484 VAL GLU ASN SER GLY ALA GLY PRO THR SER PHE LYS THR SEQRES 2 A 484 MET LYS VAL ILE ASP PRO GLN HIS SER ASP LYS PRO ASN SEQRES 3 A 484 VAL LEU ILE LEU GLY SER GLY TRP GLY ALA ILE SER PHE SEQRES 4 A 484 LEU LYS HIS ILE ASP THR LYS LYS TYR ASN VAL SER ILE SEQRES 5 A 484 ILE SER PRO ARG SER TYR PHE LEU PHE THR PRO LEU LEU SEQRES 6 A 484 PRO SER ALA PRO VAL GLY THR VAL ASP GLU LYS SER ILE SEQRES 7 A 484 ILE GLU PRO ILE VAL ASN PHE ALA LEU LYS LYS LYS GLY SEQRES 8 A 484 ASN VAL THR TYR TYR GLU ALA GLU ALA THR SER ILE ASN SEQRES 9 A 484 PRO ASP ARG ASN THR VAL THR ILE LYS SER LEU SER ALA SEQRES 10 A 484 VAL SER GLN LEU TYR GLN PRO GLU ASN HIS LEU GLY LEU SEQRES 11 A 484 HIS GLN ALA GLU PRO ALA GLU ILE LYS TYR ASP TYR LEU SEQRES 12 A 484 ILE SER ALA VAL GLY ALA GLU PRO ASN THR PHE GLY ILE SEQRES 13 A 484 PRO GLY VAL THR ASP TYR GLY HIS PHE LEU LYS GLU ILE SEQRES 14 A 484 PRO ASN SER LEU GLU ILE ARG ARG THR PHE ALA ALA ASN SEQRES 15 A 484 LEU GLU LYS ALA ASN LEU LEU PRO LYS GLY ASP PRO GLU SEQRES 16 A 484 ARG ARG ARG LEU LEU SER ILE VAL VAL VAL GLY GLY GLY SEQRES 17 A 484 PRO THR GLY VAL GLU ALA ALA GLY GLU LEU GLN ASP TYR SEQRES 18 A 484 VAL HIS GLN ASP LEU ARG LYS PHE LEU PRO ALA LEU ALA SEQRES 19 A 484 GLU GLU VAL GLN ILE HIS LEU VAL GLU ALA LEU PRO ILE SEQRES 20 A 484 VAL LEU ASN MET PHE GLU LYS LYS LEU SER SER TYR ALA SEQRES 21 A 484 GLN SER HIS LEU GLU ASN THR SER ILE LYS VAL HIS LEU SEQRES 22 A 484 ARG THR ALA VAL ALA LYS VAL GLU GLU LYS GLN LEU LEU SEQRES 23 A 484 ALA LYS THR LYS HIS GLU ASP GLY LYS ILE THR GLU GLU SEQRES 24 A 484 THR ILE PRO TYR GLY THR LEU ILE TRP ALA THR GLY ASN SEQRES 25 A 484 LYS ALA ARG PRO VAL ILE THR ASP LEU PHE LYS LYS ILE SEQRES 26 A 484 PRO GLU GLN ASN SER SER LYS ARG GLY LEU ALA VAL ASN SEQRES 27 A 484 ASP PHE LEU GLN VAL LYS GLY SER ASN ASN ILE PHE ALA SEQRES 28 A 484 ILE GLY ASP ASN ALA PHE ALA GLY LEU PRO PRO THR ALA SEQRES 29 A 484 GLN VAL ALA HIS GLN GLU ALA GLU TYR LEU ALA LYS ASN SEQRES 30 A 484 PHE ASP LYS MET ALA GLN ILE PRO ASN PHE GLN LYS ASN SEQRES 31 A 484 LEU SER SER ARG LYS ASP LYS ILE ASP LEU LEU PHE GLU SEQRES 32 A 484 GLU ASN ASN PHE LYS PRO PHE LYS TYR ASN ASP LEU GLY SEQRES 33 A 484 ALA LEU ALA TYR LEU GLY SER GLU ARG ALA ILE ALA THR SEQRES 34 A 484 ILE ARG SER GLY LYS ARG THR PHE TYR THR GLY GLY GLY SEQRES 35 A 484 LEU MET THR PHE TYR LEU TRP ARG ILE LEU TYR LEU SER SEQRES 36 A 484 MET ILE LEU SER ALA ARG SER ARG LEU LYS VAL PHE PHE SEQRES 37 A 484 ASP TRP ILE LYS LEU ALA PHE PHE LYS ARG ASP PHE PHE SEQRES 38 A 484 LYS GLY LEU HET FAD A 601 53 HET MG A 602 1 HET MG A 603 1 HET MG A 604 1 HET MG A 605 1 HET PE4 A 606 24 HET P6G A 607 19 HET GOL A 608 6 HET GOL A 609 6 HET GOL A 610 6 HET GOL A 611 6 HET PG4 A 612 13 HET PG4 A 613 13 HET PEG A 614 7 HET PEG A 615 7 HET PGE A 616 10 HET PGE A 617 10 HET PEG A 618 7 HET PGE A 619 10 HET GOL A 620 6 HET GOL A 621 6 HET GOL A 622 6 HET MES A 623 12 HET MES A 624 12 HET SMA A 625 37 HET SMA A 626 74 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM MG MAGNESIUM ION HETNAM PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}- HETNAM 2 PE4 ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL HETNAM P6G HEXAETHYLENE GLYCOL HETNAM GOL GLYCEROL HETNAM PG4 TETRAETHYLENE GLYCOL HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PGE TRIETHYLENE GLYCOL HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM SMA STIGMATELLIN A HETSYN PE4 POLYETHYLENE GLYCOL PEG4000 HETSYN P6G POLYETHYLENE GLYCOL PEG400 HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 MG 4(MG 2+) FORMUL 7 PE4 C16 H34 O8 FORMUL 8 P6G C12 H26 O7 FORMUL 9 GOL 7(C3 H8 O3) FORMUL 13 PG4 2(C8 H18 O5) FORMUL 15 PEG 3(C4 H10 O3) FORMUL 17 PGE 3(C6 H14 O4) FORMUL 24 MES 2(C6 H13 N O4 S) FORMUL 26 SMA 2(C30 H42 O7) FORMUL 28 HOH *345(H2 O) HELIX 1 AA1 GLY A 62 ILE A 72 1 11 HELIX 2 AA2 THR A 91 ALA A 97 5 7 HELIX 3 AA3 ASP A 103 SER A 106 5 4 HELIX 4 AA4 ILE A 111 LEU A 116 1 6 HELIX 5 AA5 GLY A 187 GLY A 192 1 6 HELIX 6 AA6 GLU A 197 ASN A 216 1 20 HELIX 7 AA7 ASP A 222 LEU A 229 1 8 HELIX 8 AA8 GLY A 237 ASP A 254 1 18 HELIX 9 AA9 ASP A 254 LEU A 259 1 6 HELIX 10 AB1 LEU A 259 VAL A 266 1 8 HELIX 11 AB2 GLU A 282 THR A 296 1 15 HELIX 12 AB3 ARG A 344 LYS A 352 1 9 HELIX 13 AB4 LYS A 353 ASN A 358 5 6 HELIX 14 AB5 THR A 392 ALA A 411 1 20 HELIX 15 AB6 GLN A 412 LYS A 418 5 7 HELIX 16 AB7 ASP A 428 ASN A 434 1 7 HELIX 17 AB8 LEU A 472 ILE A 486 1 15 HELIX 18 AB9 SER A 488 PHE A 505 1 18 SHEET 1 AA1 6 PHE A 40 LYS A 41 0 SHEET 2 AA1 6 VAL A 122 GLU A 126 -1 O TYR A 124 N PHE A 40 SHEET 3 AA1 6 ASN A 78 SER A 83 1 N ILE A 81 O TYR A 125 SHEET 4 AA1 6 ASN A 55 LEU A 59 1 N ILE A 58 O SER A 80 SHEET 5 AA1 6 TYR A 171 SER A 174 1 O ILE A 173 N LEU A 57 SHEET 6 AA1 6 ILE A 378 ALA A 380 1 O PHE A 379 N LEU A 172 SHEET 1 AA2 2 TYR A 87 LEU A 89 0 SHEET 2 AA2 2 ILE A 108 PRO A 110 -1 O GLU A 109 N PHE A 88 SHEET 1 AA3 3 GLU A 128 ASN A 133 0 SHEET 2 AA3 3 THR A 138 LYS A 142 -1 O THR A 140 N SER A 131 SHEET 3 AA3 3 GLU A 166 LYS A 168 -1 O ILE A 167 N VAL A 139 SHEET 1 AA4 2 GLU A 179 PRO A 180 0 SHEET 2 AA4 2 ASN A 341 LYS A 342 -1 O LYS A 342 N GLU A 179 SHEET 1 AA5 5 HIS A 193 PHE A 194 0 SHEET 2 AA5 5 THR A 334 TRP A 337 1 O TRP A 337 N HIS A 193 SHEET 3 AA5 5 SER A 230 VAL A 234 1 N VAL A 234 O ILE A 336 SHEET 4 AA5 5 GLN A 267 VAL A 271 1 O HIS A 269 N VAL A 233 SHEET 5 AA5 5 LYS A 299 HIS A 301 1 O HIS A 301 N LEU A 270 SHEET 1 AA6 3 THR A 304 VAL A 309 0 SHEET 2 AA6 3 GLN A 313 LYS A 319 -1 O LYS A 317 N ALA A 305 SHEET 3 AA6 3 ILE A 325 PRO A 331 -1 O ILE A 330 N LEU A 314 SHEET 1 AA7 2 LEU A 364 ALA A 365 0 SHEET 2 AA7 2 ALA A 385 PHE A 386 1 O PHE A 386 N LEU A 364 SHEET 1 AA8 3 GLY A 445 TYR A 449 0 SHEET 2 AA8 3 ALA A 455 SER A 461 -1 O THR A 458 N ALA A 446 SHEET 3 AA8 3 ARG A 464 GLY A 471 -1 O TYR A 467 N ILE A 459 LINK O ALA A 175 MG MG A 603 1555 1555 2.53 LINK O ILE A 381 MG MG A 602 1555 1555 2.58 LINK OD2 ASP A 383 MG MG A 605 1555 1555 2.92 LINK O2P FAD A 601 MG MG A 602 1555 1555 2.54 LINK O1P FAD A 601 MG MG A 603 1555 1555 2.61 LINK O1A FAD A 601 MG MG A 604 1555 1555 3.00 LINK O2A FAD A 601 MG MG A 604 1555 1555 2.89 LINK O2A FAD A 601 MG MG A 605 1555 1555 2.69 LINK MG MG A 604 O HOH A 731 1555 1555 2.60 LINK MG MG A 604 O HOH A 832 1555 1555 2.64 LINK MG MG A 605 O HOH A 703 1555 1555 2.72 SITE 1 AC1 41 GLY A 60 SER A 61 GLY A 62 TRP A 63 SITE 2 AC1 41 GLY A 64 ILE A 82 SER A 83 PRO A 84 SITE 3 AC1 41 ARG A 85 THR A 91 PRO A 92 GLU A 128 SITE 4 AC1 41 ALA A 129 ALA A 175 VAL A 176 GLY A 177 SITE 5 AC1 41 LEU A 195 THR A 239 ARG A 344 GLY A 382 SITE 6 AC1 41 ASP A 383 PRO A 391 THR A 392 ALA A 393 SITE 7 AC1 41 GLN A 394 TYR A 482 MG A 602 MG A 603 SITE 8 AC1 41 MG A 604 MG A 605 GOL A 608 PEG A 615 SITE 9 AC1 41 MES A 623 SMA A 626 HOH A 702 HOH A 703 SITE 10 AC1 41 HOH A 706 HOH A 736 HOH A 826 HOH A 832 SITE 11 AC1 41 HOH A 925 SITE 1 AC2 7 ALA A 175 GLY A 177 ILE A 381 GLY A 382 SITE 2 AC2 7 ASP A 383 ASN A 384 FAD A 601 SITE 1 AC3 5 GLY A 62 GLY A 64 ALA A 65 ALA A 175 SITE 2 AC3 5 FAD A 601 SITE 1 AC4 5 ARG A 85 THR A 91 FAD A 601 HOH A 731 SITE 2 AC4 5 HOH A 832 SITE 1 AC5 6 GLY A 177 ALA A 178 LYS A 196 ASP A 383 SITE 2 AC5 6 FAD A 601 HOH A 703 SITE 1 AC6 16 PRO A 37 SER A 39 PHE A 40 VAL A 112 SITE 2 AC6 16 ASN A 113 LEU A 212 ASN A 216 TYR A 250 SITE 3 AC6 16 PHE A 258 LEU A 259 ARG A 490 ASP A 508 SITE 4 AC6 16 PHE A 509 PHE A 510 HOH A 729 HOH A 735 SITE 1 AC7 3 GLU A 433 ALA A 503 SMA A 625 SITE 1 AC8 10 PRO A 238 THR A 392 ALA A 446 LEU A 447 SITE 2 AC8 10 FAD A 601 MES A 623 SMA A 626 HOH A 860 SITE 3 AC8 10 HOH A 925 HOH A 943 SITE 1 AC9 6 SER A 360 LYS A 361 ARG A 362 GLY A 363 SITE 2 AC9 6 ALA A 365 PHE A 386 SITE 1 AD1 6 LEU A 202 ARG A 206 LYS A 511 GLY A 512 SITE 2 AD1 6 LEU A 513 HOH A 805 SITE 1 AD2 6 ARG A 303 THR A 304 ALA A 305 LYS A 317 SITE 2 AD2 6 LYS A 319 HOH A 891 SITE 1 AD3 7 THR A 38 PRO A 84 ARG A 85 SER A 86 SITE 2 AD3 7 TYR A 87 GOL A 622 HOH A 714 SITE 1 AD4 6 ASP A 52 ASP A 170 ASN A 377 PHE A 416 SITE 2 AD4 6 GLN A 417 LYS A 418 SITE 1 AD5 5 PRO A 48 TYR A 288 GLY A 469 GLY A 470 SITE 2 AD5 5 HOH A 842 SITE 1 AD6 5 ARG A 344 PRO A 345 VAL A 346 FAD A 601 SITE 2 AD6 5 HOH A 726 SITE 1 AD7 1 SMA A 626 SITE 1 AD8 2 ARG A 492 PGE A 619 SITE 1 AD9 8 ILE A 185 VAL A 234 VAL A 271 ALA A 273 SITE 2 AD9 8 THR A 304 VAL A 306 HOH A 822 HOH A 848 SITE 1 AE1 3 PHE A 504 PGE A 617 HOH A 759 SITE 1 AE2 10 ASP A 249 GLN A 253 TYR A 449 GLU A 453 SITE 2 AE2 10 ARG A 479 LEU A 502 ARG A 507 HOH A 716 SITE 3 AE2 10 HOH A 749 HOH A 753 SITE 1 AE3 10 GLY A 236 GLY A 237 GLU A 272 ILE A 276 SITE 2 AE3 10 VAL A 277 LEU A 278 ASN A 279 MET A 280 SITE 3 AE3 10 HOH A 707 HOH A 807 SITE 1 AE4 6 PRO A 84 ARG A 85 GLU A 197 PG4 A 612 SITE 2 AE4 6 HOH A 709 HOH A 851 SITE 1 AE5 10 LEU A 195 PRO A 238 THR A 239 THR A 339 SITE 2 AE5 10 GLY A 340 ASN A 341 FAD A 601 GOL A 608 SITE 3 AE5 10 HOH A 723 HOH A 860 SITE 1 AE6 7 LYS A 41 MET A 43 LYS A 257 PHE A 258 SITE 2 AE6 7 LEU A 259 PRO A 260 ASN A 435 SITE 1 AE7 4 TYR A 476 ARG A 479 P6G A 607 HOH A 754 SITE 1 AE8 14 TRP A 63 PRO A 92 ALA A 393 GLN A 394 SITE 2 AE8 14 HIS A 397 LEU A 444 ILE A 459 SER A 461 SITE 3 AE8 14 TYR A 482 SER A 484 MET A 485 FAD A 601 SITE 4 AE8 14 GOL A 608 PGE A 616 CRYST1 116.670 128.456 86.711 90.00 90.00 90.00 C 2 2 21 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 0.008571 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007785 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011533 0.00000