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- PDB-4g74: Crystal structure of NDH with Quinone -

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Basic information

Entry
Database: PDB / ID: 4g74
TitleCrystal structure of NDH with Quinone
ComponentsRotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
KeywordsOXIDOREDUCTASE / Rossmann fold / electron transfer / FAD
Function / homology
Function and homology information


NADH:quinone reductase (non-electrogenic) / NADH oxidation / mitochondrial electron transport, NADH to ubiquinone / NADH dehydrogenase (ubiquinone) activity / mitochondrial inner membrane / oxidoreductase activity / mitochondrial matrix / positive regulation of apoptotic process / mitochondrion / identical protein binding
Similarity search - Function
Alternative NADH dehydrogenase / FAD/NAD(P)-binding domain - #100 / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-UQ5 / Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsLi, W. / Feng, Y. / Ge, J. / Yang, M.
CitationJournal: Nature / Year: 2012
Title: Structural insight into the type-II mitochondrial NADH dehydrogenases.
Authors: Feng, Y. / Li, W. / Li, J. / Wang, J. / Ge, J. / Xu, D. / Liu, Y. / Wu, K. / Zeng, Q. / Wu, J.W. / Tian, C. / Zhou, B. / Yang, M.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _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: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
B: Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,48823
Polymers112,1482
Non-polymers5,34021
Water6,467359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13290 Å2
ΔGint-160 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.909, 230.844, 112.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-728-

HOH

21B-747-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Rotenone-insensitive NADH-ubiquinone oxidoreductase, mitochondrial / Internal NADH dehydrogenase


Mass: 56074.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: NDI1, YML120C, YM7056.06C / Production host: Escherichia coli (E. coli)
References: UniProt: P32340, NADH:quinone reductase (non-electrogenic)

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Non-polymers , 5 types, 380 molecules

#2: Chemical
ChemComp-UQ5 / 2,3-DIMETHOXY-5-METHYL-6-(3,11,15,19-TETRAMETHYL-EICOSA-2,6,10,14,18-PENTAENYL)-[1,4]BENZOQUINONE


Mass: 522.758 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H50O4
#3: Chemical
ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE


Mass: 352.508 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 3.85 Å3/Da / Density % sol: 68.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 3.8M potassium formate, 2% w/v Polyethylene glycol monomethyl ether 2000, pH 4.2 , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 25, 2012
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 64620 / Num. obs: 62778 / % possible obs: 97.15 %
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.48-2.567196
2.567-2.672197.5
2.672-2.793198.8
2.793-2.941199.2
2.941-3.125199.6
3.125-3.366199.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID code 4G6G

4g6g


Resolution: 2.48→43.612 Å / SU ML: 0.29 / σ(F): 1.34 / Phase error: 24.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2331 3031 5.07 %
Rwork0.1949 --
obs0.1968 59747 97.15 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.56 Å2 / ksol: 0.361 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.3042 Å2-0 Å20 Å2
2---7.3159 Å2-0 Å2
3----6.9883 Å2
Refinement stepCycle: LAST / Resolution: 2.48→43.612 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7376 0 289 359 8024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087841
X-RAY DIFFRACTIONf_angle_d1.36110644
X-RAY DIFFRACTIONf_dihedral_angle_d15.4432934
X-RAY DIFFRACTIONf_chiral_restr0.1081175
X-RAY DIFFRACTIONf_plane_restr0.0051321
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4802-2.51890.3331080.2536185571
2.5189-2.56020.27231190.2568213881
2.5602-2.60440.32461320.2413243094
2.6044-2.65170.34691370.248259999
2.6517-2.70270.3081060.2351260699
2.7027-2.75790.28081450.2182262799
2.7579-2.81780.28371640.2259259799
2.8178-2.88340.25241250.2387262999
2.8834-2.95550.30051290.22212642100
2.9555-3.03540.26391330.225261199
3.0354-3.12470.28191460.2244261599
3.1247-3.22550.22451210.21692654100
3.2255-3.34070.26181650.20712597100
3.3407-3.47440.22591490.19412620100
3.4744-3.63250.21651440.17972657100
3.6325-3.82390.2551250.17432638100
3.8239-4.06330.19711410.1612668100
4.0633-4.37680.17371530.14682632100
4.3768-4.81670.17041520.13942682100
4.8167-5.51250.19441650.16872657100
5.5125-6.94070.26511310.23312739100
6.9407-43.61920.20411410.1992282399

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