HEADER OXIDOREDUCTASE 24-JUL-12 4G9K TITLE STRUCTURE OF THE NDI1 PROTEIN FROM SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ROTENONE-INSENSITIVE NADH-UBIQUINONE OXIDOREDUCTASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: INTERNAL NADH DEHYDROGENASE, NADH:UBIQUINONE REDUCTASE (NON- COMPND 5 ELECTROGENIC); COMPND 6 EC: 1.6.5.9; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: NDI1, YML120C, YM7056.06C; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS NADH:QUINONE OXIDOREDUCTASE, MEMBRANE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.IWATA,Y.LEE,T.YAMASHITA,T.YAGI,S.IWATA,A.D.CAMERON,M.J.MAHER REVDAT 3 28-FEB-24 4G9K 1 REMARK REVDAT 2 03-OCT-12 4G9K 1 JRNL REVDAT 1 05-SEP-12 4G9K 0 JRNL AUTH M.IWATA,Y.LEE,T.YAMASHITA,T.YAGI,S.IWATA,A.D.CAMERON, JRNL AUTH 2 M.J.MAHER JRNL TITL THE STRUCTURE OF THE YEAST NADH DEHYDROGENASE (NDI1) REVEALS JRNL TITL 2 OVERLAPPING BINDING SITES FOR WATER- AND LIPID-SOLUBLE JRNL TITL 3 SUBSTRATES. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 15247 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22949654 JRNL DOI 10.1073/PNAS.1210059109 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.32 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 73.7 REMARK 3 NUMBER OF REFLECTIONS : 27911 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) : 0.235 REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1401 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 592 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 22.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.3600 REMARK 3 BIN FREE R VALUE SET COUNT : 35 REMARK 3 BIN FREE R VALUE : 0.4250 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7334 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 106 REMARK 3 SOLVENT ATOMS : 18 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.94 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.38000 REMARK 3 B22 (A**2) : -17.85000 REMARK 3 B33 (A**2) : 20.23000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.285 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 31.283 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.920 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.865 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7648 ; 0.005 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5230 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10384 ; 0.959 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): 12802 ; 0.787 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 930 ; 5.289 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 332 ;31.369 ;24.337 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1324 ;13.949 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.917 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1154 ; 0.058 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8352 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1526 ; 0.001 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 43 A 513 1 REMARK 3 1 B 43 B 513 1 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 TIGHT THERMAL 1 A (A**2): 6274 ; 2.870 ; 0.500 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 43 A 513 REMARK 3 ORIGIN FOR THE GROUP (A): 21.1630 -20.3965 -17.8633 REMARK 3 T TENSOR REMARK 3 T11: 0.2169 T22: 0.2298 REMARK 3 T33: 0.0649 T12: -0.0235 REMARK 3 T13: 0.0471 T23: -0.0937 REMARK 3 L TENSOR REMARK 3 L11: 2.3487 L22: 2.1761 REMARK 3 L33: 1.3553 L12: -0.4245 REMARK 3 L13: 0.0487 L23: -0.1914 REMARK 3 S TENSOR REMARK 3 S11: 0.0542 S12: -0.1701 S13: 0.2709 REMARK 3 S21: 0.1239 S22: 0.0315 S23: -0.1038 REMARK 3 S31: -0.1408 S32: 0.1782 S33: -0.0857 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 43 B 513 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3237 -59.7252 -14.9974 REMARK 3 T TENSOR REMARK 3 T11: 0.2255 T22: 0.2477 REMARK 3 T33: 0.0472 T12: 0.0127 REMARK 3 T13: -0.0117 T23: 0.0752 REMARK 3 L TENSOR REMARK 3 L11: 2.8851 L22: 2.3241 REMARK 3 L33: 2.1831 L12: -0.1453 REMARK 3 L13: 0.4656 L23: -0.1098 REMARK 3 S TENSOR REMARK 3 S11: 0.0358 S12: -0.1565 S13: -0.3019 REMARK 3 S21: 0.1954 S22: -0.0236 S23: 0.0125 REMARK 3 S31: 0.2867 S32: 0.2865 S33: -0.0123 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 4G9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-12. REMARK 100 THE DEPOSITION ID IS D_1000073909. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35714 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 34% PEG 400, 100 MM NACL, 2% ETHYLENE REMARK 280 GLYCOL, 5% GLYCEROL, 50 MM MES, PH 6.0, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 58.06000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 35.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 82.78000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 58.06000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 82.78000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 39330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -44.0 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 LYS A 418 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 465 LYS B 418 REMARK 465 ASN B 419 REMARK 465 LEU B 420 REMARK 465 SER B 421 REMARK 465 SER B 422 REMARK 465 ARG B 423 REMARK 465 LYS B 424 REMARK 465 ASP B 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 LYS A 44 105.96 62.64 REMARK 500 HIS A 50 -50.81 -121.88 REMARK 500 SER A 61 46.31 -142.20 REMARK 500 GLU A 154 -120.37 -144.26 REMARK 500 THR A 339 -118.58 -125.80 REMARK 500 LYS A 361 -61.48 -140.81 REMARK 500 ASN A 435 73.08 56.61 REMARK 500 PHE A 466 72.95 -155.03 REMARK 500 LYS A 506 72.81 49.00 REMARK 500 ARG A 507 133.08 72.42 REMARK 500 LYS B 44 105.97 63.37 REMARK 500 HIS B 50 -50.71 -121.94 REMARK 500 SER B 61 45.90 -143.45 REMARK 500 GLU B 154 -119.92 -144.19 REMARK 500 THR B 339 -118.85 -125.34 REMARK 500 LYS B 361 -61.37 -140.20 REMARK 500 ASN B 435 72.42 56.48 REMARK 500 PHE B 466 72.97 -154.30 REMARK 500 LYS B 506 72.83 48.32 REMARK 500 ARG B 507 133.41 72.70 REMARK 500 REMARK 500 REMARK: NULL 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 FAD B 601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GAP RELATED DB: PDB REMARK 900 RELATED ID: 4GAV RELATED DB: PDB DBREF 4G9K A 43 513 UNP P32340 NDI1_YEAST 43 513 DBREF 4G9K B 43 513 UNP P32340 NDI1_YEAST 43 513 SEQRES 1 A 471 MET LYS VAL ILE ASP PRO GLN HIS SER ASP LYS PRO ASN SEQRES 2 A 471 VAL LEU ILE LEU GLY SER GLY TRP GLY ALA ILE SER PHE SEQRES 3 A 471 LEU LYS HIS ILE ASP THR LYS LYS TYR ASN VAL SER ILE SEQRES 4 A 471 ILE SER PRO ARG SER TYR PHE LEU PHE THR PRO LEU LEU SEQRES 5 A 471 PRO SER ALA PRO VAL GLY THR VAL ASP GLU LYS SER ILE SEQRES 6 A 471 ILE GLU PRO ILE VAL ASN PHE ALA LEU LYS LYS LYS GLY SEQRES 7 A 471 ASN VAL THR TYR TYR GLU ALA GLU ALA THR SER ILE ASN SEQRES 8 A 471 PRO ASP ARG ASN THR VAL THR ILE LYS SER LEU SER ALA SEQRES 9 A 471 VAL SER GLN LEU TYR GLN PRO GLU ASN HIS LEU GLY LEU SEQRES 10 A 471 HIS GLN ALA GLU PRO ALA GLU ILE LYS TYR ASP TYR LEU SEQRES 11 A 471 ILE SER ALA VAL GLY ALA GLU PRO ASN THR PHE GLY ILE SEQRES 12 A 471 PRO GLY VAL THR ASP TYR GLY HIS PHE LEU LYS GLU ILE SEQRES 13 A 471 PRO ASN SER LEU GLU ILE ARG ARG THR PHE ALA ALA ASN SEQRES 14 A 471 LEU GLU LYS ALA ASN LEU LEU PRO LYS GLY ASP PRO GLU SEQRES 15 A 471 ARG ARG ARG LEU LEU SER ILE VAL VAL VAL GLY GLY GLY SEQRES 16 A 471 PRO THR GLY VAL GLU ALA ALA GLY GLU LEU GLN ASP TYR SEQRES 17 A 471 VAL HIS GLN ASP LEU ARG LYS PHE LEU PRO ALA LEU ALA SEQRES 18 A 471 GLU GLU VAL GLN ILE HIS LEU VAL GLU ALA LEU PRO ILE SEQRES 19 A 471 VAL LEU ASN MET PHE GLU LYS LYS LEU SER SER TYR ALA SEQRES 20 A 471 GLN SER HIS LEU GLU ASN THR SER ILE LYS VAL HIS LEU SEQRES 21 A 471 ARG THR ALA VAL ALA LYS VAL GLU GLU LYS GLN LEU LEU SEQRES 22 A 471 ALA LYS THR LYS HIS GLU ASP GLY LYS ILE THR GLU GLU SEQRES 23 A 471 THR ILE PRO TYR GLY THR LEU ILE TRP ALA THR GLY ASN SEQRES 24 A 471 LYS ALA ARG PRO VAL ILE THR ASP LEU PHE LYS LYS ILE SEQRES 25 A 471 PRO GLU GLN ASN SER SER LYS ARG GLY LEU ALA VAL ASN SEQRES 26 A 471 ASP PHE LEU GLN VAL LYS GLY SER ASN ASN ILE PHE ALA SEQRES 27 A 471 ILE GLY ASP ASN ALA PHE ALA GLY LEU PRO PRO THR ALA SEQRES 28 A 471 GLN VAL ALA HIS GLN GLU ALA GLU TYR LEU ALA LYS ASN SEQRES 29 A 471 PHE ASP LYS MET ALA GLN ILE PRO ASN PHE GLN LYS ASN SEQRES 30 A 471 LEU SER SER ARG LYS ASP LYS ILE ASP LEU LEU PHE GLU SEQRES 31 A 471 GLU ASN ASN PHE LYS PRO PHE LYS TYR ASN ASP LEU GLY SEQRES 32 A 471 ALA LEU ALA TYR LEU GLY SER GLU ARG ALA ILE ALA THR SEQRES 33 A 471 ILE ARG SER GLY LYS ARG THR PHE TYR THR GLY GLY GLY SEQRES 34 A 471 LEU MET THR PHE TYR LEU TRP ARG ILE LEU TYR LEU SER SEQRES 35 A 471 MET ILE LEU SER ALA ARG SER ARG LEU LYS VAL PHE PHE SEQRES 36 A 471 ASP TRP ILE LYS LEU ALA PHE PHE LYS ARG ASP PHE PHE SEQRES 37 A 471 LYS GLY LEU SEQRES 1 B 471 MET LYS VAL ILE ASP PRO GLN HIS SER ASP LYS PRO ASN SEQRES 2 B 471 VAL LEU ILE LEU GLY SER GLY TRP GLY ALA ILE SER PHE SEQRES 3 B 471 LEU LYS HIS ILE ASP THR LYS LYS TYR ASN VAL SER ILE SEQRES 4 B 471 ILE SER PRO ARG SER TYR PHE LEU PHE THR PRO LEU LEU SEQRES 5 B 471 PRO SER ALA PRO VAL GLY THR VAL ASP GLU LYS SER ILE SEQRES 6 B 471 ILE GLU PRO ILE VAL ASN PHE ALA LEU LYS LYS LYS GLY SEQRES 7 B 471 ASN VAL THR TYR TYR GLU ALA GLU ALA THR SER ILE ASN SEQRES 8 B 471 PRO ASP ARG ASN THR VAL THR ILE LYS SER LEU SER ALA SEQRES 9 B 471 VAL SER GLN LEU TYR GLN PRO GLU ASN HIS LEU GLY LEU SEQRES 10 B 471 HIS GLN ALA GLU PRO ALA GLU ILE LYS TYR ASP TYR LEU SEQRES 11 B 471 ILE SER ALA VAL GLY ALA GLU PRO ASN THR PHE GLY ILE SEQRES 12 B 471 PRO GLY VAL THR ASP TYR GLY HIS PHE LEU LYS GLU ILE SEQRES 13 B 471 PRO ASN SER LEU GLU ILE ARG ARG THR PHE ALA ALA ASN SEQRES 14 B 471 LEU GLU LYS ALA ASN LEU LEU PRO LYS GLY ASP PRO GLU SEQRES 15 B 471 ARG ARG ARG LEU LEU SER ILE VAL VAL VAL GLY GLY GLY SEQRES 16 B 471 PRO THR GLY VAL GLU ALA ALA GLY GLU LEU GLN ASP TYR SEQRES 17 B 471 VAL HIS GLN ASP LEU ARG LYS PHE LEU PRO ALA LEU ALA SEQRES 18 B 471 GLU GLU VAL GLN ILE HIS LEU VAL GLU ALA LEU PRO ILE SEQRES 19 B 471 VAL LEU ASN MET PHE GLU LYS LYS LEU SER SER TYR ALA SEQRES 20 B 471 GLN SER HIS LEU GLU ASN THR SER ILE LYS VAL HIS LEU SEQRES 21 B 471 ARG THR ALA VAL ALA LYS VAL GLU GLU LYS GLN LEU LEU SEQRES 22 B 471 ALA LYS THR LYS HIS GLU ASP GLY LYS ILE THR GLU GLU SEQRES 23 B 471 THR ILE PRO TYR GLY THR LEU ILE TRP ALA THR GLY ASN SEQRES 24 B 471 LYS ALA ARG PRO VAL ILE THR ASP LEU PHE LYS LYS ILE SEQRES 25 B 471 PRO GLU GLN ASN SER SER LYS ARG GLY LEU ALA VAL ASN SEQRES 26 B 471 ASP PHE LEU GLN VAL LYS GLY SER ASN ASN ILE PHE ALA SEQRES 27 B 471 ILE GLY ASP ASN ALA PHE ALA GLY LEU PRO PRO THR ALA SEQRES 28 B 471 GLN VAL ALA HIS GLN GLU ALA GLU TYR LEU ALA LYS ASN SEQRES 29 B 471 PHE ASP LYS MET ALA GLN ILE PRO ASN PHE GLN LYS ASN SEQRES 30 B 471 LEU SER SER ARG LYS ASP LYS ILE ASP LEU LEU PHE GLU SEQRES 31 B 471 GLU ASN ASN PHE LYS PRO PHE LYS TYR ASN ASP LEU GLY SEQRES 32 B 471 ALA LEU ALA TYR LEU GLY SER GLU ARG ALA ILE ALA THR SEQRES 33 B 471 ILE ARG SER GLY LYS ARG THR PHE TYR THR GLY GLY GLY SEQRES 34 B 471 LEU MET THR PHE TYR LEU TRP ARG ILE LEU TYR LEU SER SEQRES 35 B 471 MET ILE LEU SER ALA ARG SER ARG LEU LYS VAL PHE PHE SEQRES 36 B 471 ASP TRP ILE LYS LEU ALA PHE PHE LYS ARG ASP PHE PHE SEQRES 37 B 471 LYS GLY LEU HET FAD A 601 53 HET FAD B 601 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 3 FAD 2(C27 H33 N9 O15 P2) FORMUL 5 HOH *18(H2 O) HELIX 1 1 GLY A 62 ILE A 72 1 11 HELIX 2 2 THR A 91 ALA A 97 5 7 HELIX 3 3 GLU A 104 SER A 106 5 3 HELIX 4 4 ILE A 111 LYS A 118 1 8 HELIX 5 5 GLY A 187 GLY A 192 1 6 HELIX 6 6 GLU A 197 LEU A 217 1 21 HELIX 7 7 ASP A 222 LEU A 229 1 8 HELIX 8 8 GLY A 237 ASP A 254 1 18 HELIX 9 9 ASP A 254 LEU A 259 1 6 HELIX 10 10 LEU A 259 VAL A 266 1 8 HELIX 11 11 GLU A 282 THR A 296 1 15 HELIX 12 12 ARG A 344 ILE A 354 1 11 HELIX 13 13 PRO A 355 ASN A 358 5 4 HELIX 14 14 THR A 392 ILE A 413 1 22 HELIX 15 15 PRO A 414 GLN A 417 5 4 HELIX 16 16 ILE A 427 ASN A 434 1 8 HELIX 17 17 GLY A 471 MET A 485 1 15 HELIX 18 18 SER A 488 LYS A 506 1 19 HELIX 19 19 GLY B 62 ILE B 72 1 11 HELIX 20 20 THR B 91 ALA B 97 5 7 HELIX 21 21 GLU B 104 SER B 106 5 3 HELIX 22 22 ILE B 111 LYS B 118 1 8 HELIX 23 23 GLY B 187 GLY B 192 1 6 HELIX 24 24 GLU B 197 LEU B 217 1 21 HELIX 25 25 ASP B 222 LEU B 229 1 8 HELIX 26 26 GLY B 237 ASP B 254 1 18 HELIX 27 27 ASP B 254 LEU B 259 1 6 HELIX 28 28 LEU B 259 VAL B 266 1 8 HELIX 29 29 GLU B 282 THR B 296 1 15 HELIX 30 30 ARG B 344 ILE B 354 1 11 HELIX 31 31 PRO B 355 ASN B 358 5 4 HELIX 32 32 THR B 392 ILE B 413 1 22 HELIX 33 33 PRO B 414 GLN B 417 5 4 HELIX 34 34 ILE B 427 ASN B 434 1 8 HELIX 35 35 GLY B 471 MET B 485 1 15 HELIX 36 36 SER B 488 LYS B 506 1 19 SHEET 1 A 8 VAL A 45 ILE A 46 0 SHEET 2 A 8 ALA A 165 LYS A 168 1 O LYS A 168 N ILE A 46 SHEET 3 A 8 THR A 138 LEU A 150 -1 N ILE A 141 O ALA A 165 SHEET 4 A 8 VAL A 122 ASN A 133 -1 N GLU A 126 O SER A 145 SHEET 5 A 8 ASN A 78 SER A 83 1 N ILE A 81 O THR A 123 SHEET 6 A 8 ASN A 55 LEU A 59 1 N ILE A 58 O SER A 80 SHEET 7 A 8 TYR A 171 SER A 174 1 O ILE A 173 N LEU A 59 SHEET 8 A 8 ILE A 378 ALA A 380 1 O PHE A 379 N LEU A 172 SHEET 1 B 2 TYR A 87 LEU A 89 0 SHEET 2 B 2 ILE A 108 PRO A 110 -1 O GLU A 109 N PHE A 88 SHEET 1 C 2 GLU A 179 PRO A 180 0 SHEET 2 C 2 ASN A 341 LYS A 342 -1 O LYS A 342 N GLU A 179 SHEET 1 D 5 HIS A 193 PHE A 194 0 SHEET 2 D 5 THR A 334 TRP A 337 1 O TRP A 337 N HIS A 193 SHEET 3 D 5 SER A 230 VAL A 234 1 N VAL A 234 O ILE A 336 SHEET 4 D 5 GLN A 267 VAL A 271 1 O HIS A 269 N ILE A 231 SHEET 5 D 5 ILE A 298 HIS A 301 1 O HIS A 301 N LEU A 270 SHEET 1 E 3 THR A 304 VAL A 309 0 SHEET 2 E 3 GLN A 313 LYS A 319 -1 O LYS A 317 N ALA A 305 SHEET 3 E 3 ILE A 325 PRO A 331 -1 O GLU A 328 N ALA A 316 SHEET 1 F 2 LEU A 364 ALA A 365 0 SHEET 2 F 2 ALA A 385 PHE A 386 1 O PHE A 386 N LEU A 364 SHEET 1 G 3 GLY A 445 TYR A 449 0 SHEET 2 G 3 ALA A 455 SER A 461 -1 O ILE A 456 N ALA A 448 SHEET 3 G 3 ARG A 464 THR A 465 -1 O ARG A 464 N SER A 461 SHEET 1 H 8 VAL B 45 ILE B 46 0 SHEET 2 H 8 ALA B 165 LYS B 168 1 O LYS B 168 N ILE B 46 SHEET 3 H 8 THR B 138 LEU B 150 -1 N ILE B 141 O ALA B 165 SHEET 4 H 8 VAL B 122 ASN B 133 -1 N GLU B 126 O SER B 145 SHEET 5 H 8 ASN B 78 SER B 83 1 N ILE B 81 O THR B 123 SHEET 6 H 8 ASN B 55 LEU B 59 1 N ILE B 58 O SER B 80 SHEET 7 H 8 TYR B 171 SER B 174 1 O ILE B 173 N LEU B 59 SHEET 8 H 8 ILE B 378 ALA B 380 1 O PHE B 379 N SER B 174 SHEET 1 I 2 TYR B 87 LEU B 89 0 SHEET 2 I 2 ILE B 108 PRO B 110 -1 O GLU B 109 N PHE B 88 SHEET 1 J 2 GLU B 179 PRO B 180 0 SHEET 2 J 2 ASN B 341 LYS B 342 -1 O LYS B 342 N GLU B 179 SHEET 1 K 5 HIS B 193 PHE B 194 0 SHEET 2 K 5 THR B 334 TRP B 337 1 O TRP B 337 N HIS B 193 SHEET 3 K 5 SER B 230 VAL B 234 1 N VAL B 232 O ILE B 336 SHEET 4 K 5 GLN B 267 VAL B 271 1 O HIS B 269 N ILE B 231 SHEET 5 K 5 LYS B 299 HIS B 301 1 O HIS B 301 N LEU B 270 SHEET 1 L 3 THR B 304 VAL B 309 0 SHEET 2 L 3 GLN B 313 LYS B 319 -1 O LYS B 317 N ALA B 305 SHEET 3 L 3 ILE B 325 PRO B 331 -1 O GLU B 328 N ALA B 316 SHEET 1 M 2 LEU B 364 ALA B 365 0 SHEET 2 M 2 ALA B 385 PHE B 386 1 O PHE B 386 N LEU B 364 SHEET 1 N 3 GLY B 445 TYR B 449 0 SHEET 2 N 3 ALA B 455 SER B 461 -1 O ILE B 456 N ALA B 448 SHEET 3 N 3 ARG B 464 THR B 465 -1 O ARG B 464 N SER B 461 SITE 1 AC1 29 GLY A 60 SER A 61 GLY A 62 TRP A 63 SITE 2 AC1 29 GLY A 64 ILE A 82 SER A 83 PRO A 84 SITE 3 AC1 29 ARG A 85 THR A 91 PRO A 92 GLU A 128 SITE 4 AC1 29 ALA A 129 ALA A 175 VAL A 176 GLY A 177 SITE 5 AC1 29 LEU A 195 THR A 239 ARG A 344 VAL A 346 SITE 6 AC1 29 GLY A 382 ASP A 383 PRO A 391 THR A 392 SITE 7 AC1 29 ALA A 393 GLN A 394 ALA A 396 TYR A 482 SITE 8 AC1 29 HOH A 701 SITE 1 AC2 27 GLY B 60 SER B 61 GLY B 62 TRP B 63 SITE 2 AC2 27 GLY B 64 ILE B 82 SER B 83 PRO B 84 SITE 3 AC2 27 ARG B 85 THR B 91 PRO B 92 GLU B 128 SITE 4 AC2 27 ALA B 129 ALA B 175 VAL B 176 GLY B 177 SITE 5 AC2 27 LEU B 195 THR B 239 ARG B 344 VAL B 346 SITE 6 AC2 27 GLY B 382 ASP B 383 PRO B 391 THR B 392 SITE 7 AC2 27 ALA B 393 GLN B 394 TYR B 482 CRYST1 116.120 165.560 70.000 90.00 90.00 90.00 P 21 21 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 0.008612 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006040 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014286 0.00000