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- PDB-2r6h: Crystal structure of the domain comprising the NAD binding and th... -

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Basic information

Entry
Database: PDB / ID: 2r6h
TitleCrystal structure of the domain comprising the NAD binding and the FAD binding regions of the NADH:ubiquinone oxidoreductase, Na translocating, F subunit from Porphyromonas gingivalis
ComponentsNADH:ubiquinone oxidoreductase, Na translocating, F subunit
KeywordsOXIDOREDUCTASE / alpha-beta-alpha sandwich / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Iron / Iron-sulfur / Metal-binding / Ubiquinone
Function / homology
Function and homology information


NADH:ubiquinone reductase (Na+-transporting) / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / sodium ion transport / 2 iron, 2 sulfur cluster binding / electron transfer activity / nucleotide binding / metal ion binding / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain ...Na(+)-translocating NADH-quinone reductase subunit F / Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain / Oxidoreductase FAD-binding domain / Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module / 2Fe-2S iron-sulfur cluster binding domain / Translation factors / Beta-grasp domain superfamily / Elongation Factor Tu (Ef-tu); domain 3 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / 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 / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.95 Å
AuthorsKim, Y. / Mulligan, R. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Domain Comprising the Regions Binding NAD and FAD from the NADH:Ubiquinone Oxidoreductase, Na Translocating, F Subunit from Porphyromonas gingivalis.
Authors: Kim, Y. / Mulligan, R. / Moy, S. / Joachimiak, A.
History
DepositionSep 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
B: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
C: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
D: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,47719
Polymers135,2784
Non-polymers4,19915
Water4,576254
1
A: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8935
Polymers33,8191
Non-polymers1,0744
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7974
Polymers33,8191
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9896
Polymers33,8191
Non-polymers1,1705
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: NADH:ubiquinone oxidoreductase, Na translocating, F subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7974
Polymers33,8191
Non-polymers9783
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)175.681, 175.681, 244.292
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
DetailsAuthors state that the biological unit is unknown.

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Components

#1: Protein
NADH:ubiquinone oxidoreductase, Na translocating, F subunit


Mass: 33819.438 Da / Num. of mol.: 4 / Fragment: The NAD and FAD binding region: Residues 126-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: nqrF, PG_2177 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q7MT22, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.48 Å3/Da / Density % sol: 64.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 2M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9794 Å
DetectorType: SBC-3 / Detector: CCD / Date: Dec 18, 2006 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.95→47.54 Å / Num. all: 40721 / Num. obs: 40721 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.5 % / Rsym value: 0.179 / Net I/σ(I): 5.2
Reflection shellResolution: 2.95→3.06 Å / Redundancy: 16.8 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 3999 / Rsym value: 0.736 / % possible all: 100

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Processing

Software
NameClassification
SBC-Collectdata collection
HKL-2000data collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.95→47.54 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 3824 10.1 %RANDOM
Rwork0.215 ---
all0.221 34054 --
obs0.221 34054 93.7 %-
Displacement parametersBiso mean: 47.411 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2---0.56 Å20 Å2
3---1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.95→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9277 0 267 254 9798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg0.685
X-RAY DIFFRACTIONf_dihedral_angle_d13.85
LS refinement shellResolution: 2.95→3.03 Å
RfactorNum. reflection% reflection
Rfree0.368 283 -
Rwork0.297 --
obs-2777 94.8 %

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