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- PDB-3w2e: Crystal structure of oxidation intermediate (20 min) of NADH-cyto... -

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Basic information

Entry
Database: PDB / ID: 3w2e
TitleCrystal structure of oxidation intermediate (20 min) of NADH-cytochrome b5 reductase from pig liver
ComponentsNADH-cytochrome b5 reductase 3
KeywordsOXIDOREDUCTASE / Reductase / cytochrome b5
Function / homology
Function and homology information


cytochrome-b5 reductase / cytochrome-b5 reductase activity, acting on NAD(P)H / cholesterol biosynthetic process / FAD binding / flavin adenine dinucleotide binding / mitochondrial outer membrane / endoplasmic reticulum membrane / mitochondrion
Similarity search - Function
NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type ...NADH:cytochrome b5 reductase-like / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / Translation factors / Elongation Factor Tu (Ef-tu); domain 3 / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADH-cytochrome b5 reductase 3
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsYamada, M. / Tamada, T. / Matsumoto, F. / Shoyama, Y. / Kimura, S. / Kuroki, R. / Miki, K.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Elucidations of the catalytic cycle of NADH-cytochrome b5 reductase by X-ray crystallography: new insights into regulation of efficient electron transfer
Authors: Yamada, M. / Tamada, T. / Takeda, K. / Matsumoto, F. / Ohno, H. / Kosugi, M. / Takaba, K. / Shoyama, Y. / Kimura, S. / Kuroki, R. / Miki, K.
History
DepositionNov 28, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NADH-cytochrome b5 reductase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2363
Polymers30,7871
Non-polymers1,4492
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.704, 73.094, 85.493
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein NADH-cytochrome b5 reductase 3 / B5R / Cytochrome b5 reductase / Diaphorase-1


Mass: 30786.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: CYB5R3, DIA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P83686, cytochrome-b5 reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 70%(v/v) MPD, 0.1M HEPES-NaOH pH 6.5, 25mM NADH, 1mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2012
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 21466 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.14 Å / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.automr: 1.8_1069)model building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8_1069phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→36.547 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8609 / SU ML: 0.19 / σ(F): 1.34 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 2000 9.33 %
Rwork0.1754 --
obs0.1789 21434 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.46 Å2 / Biso mean: 26.9929 Å2 / Biso min: 6.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2165 0 97 140 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072330
X-RAY DIFFRACTIONf_angle_d1.2363181
X-RAY DIFFRACTIONf_dihedral_angle_d18.138892
X-RAY DIFFRACTIONf_chiral_restr0.076342
X-RAY DIFFRACTIONf_plane_restr0.006402
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0987-2.15120.24811400.20061361150196
2.1512-2.20930.25141380.19171339147798
2.2093-2.27440.24871390.18851354149398
2.2744-2.34770.22011410.19221370151198
2.3477-2.43160.23091390.18911351149098
2.4316-2.5290.25981430.1851380152398
2.529-2.6440.21081400.17981370151099
2.644-2.78340.2311410.18521370151198
2.7834-2.95770.22181420.17961387152999
2.9577-3.1860.22421440.17991394153899
3.186-3.50640.2051460.17231407155399
3.5064-4.01320.18731450.15681410155599
4.0132-5.05410.16171470.15141436158399
5.0541-36.55250.25261550.19341505166099
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.6393-0.8338-0.41084.1592-0.26691.51990.38750.22470.2636-1.1928-0.44350.08180.2693-0.44380.08520.21010.09240.05220.2860.010.1458-26.45948.6813-10.3245
21.69360.13220.1552.05340.24722.16680.19910.1660.2511-0.4573-0.20570.10060.2288-0.6618-0.01270.09550.0760.0280.15770.0570.1593-22.702110.0919-8.4668
31.63970.2528-0.44233.3277-0.12792.5259-0.2746-0.1561-0.6382-0.0121-0.06560.2630.9158-0.1553-0.0370.3848-0.14820.07540.20850.01520.255-24.2387-7.9683-5.5374
40.75860.01320.23350.85460.74190.69120.0681-0.3394-0.05990.01570.0319-0.2116-0.29730.0991-0.01740.0743-0.02540.03830.1940.00960.2061-8.385816.2889-9.1773
51.3054-0.1174-0.692.20210.3491.4483-0.12330.13470.0259-0.48540.1456-0.02820.1036-0.00450.00310.2123-0.00250.00510.15450.01840.0893-11.82065.1391-24.0963
61.7914-0.4001-0.01712.1027-0.26211.4925-0.31790.0048-0.1365-0.36670.4767-0.71920.35310.5572-0.03950.22050.12040.0530.2425-0.09530.2431-0.8757-0.4874-21.4157
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 34 )A2 - 34
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 82 )A35 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 109 )A83 - 109
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 144 )A110 - 144
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 199 )A145 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 272 )A200 - 272

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