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- PDB-3w2f: Crystal structure of oxidation intermediate (10 min) of NADH-cyto... -

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Basic information

Entry
Database: PDB / ID: 3w2f
TitleCrystal structure of oxidation intermediate (10 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: 1.76 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

Downloads & links

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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
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.456, 73.014, 85.621
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


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


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
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: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 20, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 36243 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.76→1.79 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata 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: 1.76→30.813 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8811 / SU ML: 0.14 / σ(F): 0 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1916 1943 5.53 %
Rwork0.164 --
obs0.1655 35131 96.42 %
Solvent computationShrinkage radii: 1.1 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.51 Å2 / Biso mean: 25.9382 Å2 / Biso min: 8.7 Å2
Refinement stepCycle: LAST / Resolution: 1.76→30.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2153 0 97 274 2524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072330
X-RAY DIFFRACTIONf_angle_d1.2523186
X-RAY DIFFRACTIONf_dihedral_angle_d18.008887
X-RAY DIFFRACTIONf_chiral_restr0.08343
X-RAY DIFFRACTIONf_plane_restr0.006405
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 (%)
1.7597-1.80370.21721320.19482176230890
1.8037-1.85250.20091280.1882225235392
1.8525-1.9070.20141330.18032289242294
1.907-1.96850.19651360.16652300243695
1.9685-2.03880.21761360.16852333246996
2.0388-2.12050.17221380.15822362250097
2.1205-2.21690.19341370.15792394253198
2.2169-2.33380.20731410.1612391253299
2.3338-2.47990.20951390.16462419255898
2.4799-2.67130.20261440.16862439258399
2.6713-2.93990.20231440.16522437258199
2.9399-3.36490.17821450.151824642609100
3.3649-4.23770.16761450.14692482262798
4.2377-30.81780.19931450.182477262294
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)
12.61710.8433-0.86283.7465-2.04972.54010.0497-0.1360.04930.3079-0.1882-0.27720.00640.47980.10270.10090.0362-0.00980.2374-0.02260.162426.3358.851610.3345
22.8190.1995-0.86061.9583-0.91350.6920.0375-0.29490.36770.1971-0.0768-0.3051-0.33540.5323-0.02320.1283-0.0655-0.02310.2348-0.0290.230523.008317.604611.4524
33.7496-0.5484-1.1315.22.50625.6810.06060.21-0.0964-0.33370.0717-0.3340.28920.3199-0.09650.11270.04160.00840.13620.00130.113522.03382.5205-0.9554
42.0349-0.1834-0.95131.7733-0.75222.05-0.071-0.065-0.2059-0.0785-0.1205-0.3360.4850.47790.04710.19420.10260.01020.20540.0110.172924.33040.54348.5021
50.6311-0.06490.27291.7397-0.67371.9420.05030.09140.07850.24280.15770.3348-0.4371-0.4562-0.12170.1190.05950.03810.20860.03640.22624.329817.804111.5247
61.46340.0913-0.87722.9004-0.24262.4553-0.0394-0.19090.06920.48680.0611-0.1650.06940.1041-0.02890.17810.0239-0.02640.14110.00010.111411.98225.416724.319
72.28880.37910.07812.8126-1.26832.07610.031-0.1797-0.270.65340.02940.01150.6056-0.1839-0.11170.3414-0.00710.02770.17730.02620.15697.3254-5.021527.6253
82.1387-0.2467-0.69371.6396-0.30512.1038-0.03490.1362-0.0680.07370.11680.59360.3863-0.83910.01150.1836-0.0770.03340.34720.04750.2959-2.82442.43117.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 2:34)A2 - 34
2X-RAY DIFFRACTION2chain 'A' and (resseq 35:49)A35 - 49
3X-RAY DIFFRACTION3chain 'A' and (resseq 50:65)A50 - 65
4X-RAY DIFFRACTION4chain 'A' and (resseq 66:114)A66 - 114
5X-RAY DIFFRACTION5chain 'A' and (resseq 115:144)A115 - 144
6X-RAY DIFFRACTION6chain 'A' and (resseq 145:199)A145 - 199
7X-RAY DIFFRACTION7chain 'A' and (resseq 200:225)A200 - 225
8X-RAY DIFFRACTION8chain 'A' and (resseq 226:272)A226 - 272

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