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- PDB-4uaj: Crystal structure of NqrF in hexagonal space group -

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Basic information

Entry
Database: PDB / ID: 4uaj
TitleCrystal structure of NqrF in hexagonal space group
ComponentsNa(+)-translocating NADH-quinone reductase subunit F
KeywordsOXIDOREDUCTASE / Vibrio cholerae / sodium translocation / NQR
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 / FAD binding / 2 iron, 2 sulfur cluster binding / electron transfer activity / 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 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily ...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 / 2Fe-2S ferredoxin-type iron-sulfur binding domain profile. / 2Fe-2S ferredoxin-type iron-sulfur binding domain / 2Fe-2S ferredoxin-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / 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 speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7019 Å
AuthorsFritz, G.
CitationJournal: Nature / Year: 2014
Title: Structure of the V. cholerae Na+-pumping NADH:quinone oxidoreductase.
Authors: Steuber, J. / Vohl, G. / Casutt, M.S. / Vorburger, T. / Diederichs, K. / Fritz, G.
History
DepositionAug 10, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / reflns_shell
Item: _exptl_crystal_grow.temp / _reflns_shell.percent_possible_all
Revision 1.2Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3104
Polymers32,3331
Non-polymers9783
Water90150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-39 kcal/mol
Surface area13190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.220, 145.220, 90.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Na(+)-translocating NADH-quinone reductase subunit F / Na(+)-translocating NQR subunit F / NQR complex subunit F / NQR-1 subunit F


Mass: 32332.531 Da / Num. of mol.: 1 / Fragment: UNP residues 129-408
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: nqrF, VC0395_A1879, VC395_2406 / Plasmid: pBAD / Production host: Vibrio cholerae (bacteria)
References: UniProt: A5F5Y4, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 4.24 Å3/Da / Density % sol: 71 % / Description: Hexagonal crystals
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop
Details: 0.1 M MES NaOH pH 6.6, 2.2 M (NH4)2SO4, 0.6% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.7→47.534 Å / Num. obs: 15815 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 23.7 % / Biso Wilson estimate: 52.41 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.227 / Rrim(I) all: 0.232 / Χ2: 0.981 / Net I/σ(I): 18.05 / Num. measured all: 375456
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.7-2.80.5861.4272.636085160815431.45996
2.8-2.90.7331.2523.1133818139013891.27899.9
2.9-30.881.0163.9429379120712081.038100
3-3.40.9560.6836.0986444356035600.698100
3.4-3.60.9880.3711.7729657123312330.378100
3.6-40.9970.2218.8843505181218120.225100
4-50.9990.1133.3356837240624060.113100
5-60.9990.134.9625115107710770.102100
6-1010.06148.8627330121312130.062100
1010.03266.6172863803740.03298.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
PDB_EXTRACT3.14data extraction
XSCALEdata scaling
PHASERphasing
XSCALEdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4U9U

4u9u


Resolution: 2.7019→47.534 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 790 5 %Random selection
Rwork0.1892 ---
obs0.1914 15810 99.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7019→47.534 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2245 0 63 50 2358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022378
X-RAY DIFFRACTIONf_angle_d0.5163233
X-RAY DIFFRACTIONf_dihedral_angle_d15.287873
X-RAY DIFFRACTIONf_chiral_restr0.035318
X-RAY DIFFRACTIONf_plane_restr0.004417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7019-2.87120.31711270.2922412X-RAY DIFFRACTION99
2.8712-3.09280.32421290.25272458X-RAY DIFFRACTION100
3.0928-3.4040.26881300.21522474X-RAY DIFFRACTION100
3.404-3.89640.21521310.17572482X-RAY DIFFRACTION100
3.8964-4.90820.20071330.14692517X-RAY DIFFRACTION100
4.9082-47.54170.2121400.18052677X-RAY DIFFRACTION100
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)
12.20210.31030.24946.43280.51840.6428-0.0399-0.02830.3493-0.4744-0.16840.3858-0.7241-0.4650.27660.99780.0836-0.06750.3271-0.07890.479370.7921-5.9727-7.3116
24.4302-1.05430.90045.1892-0.85072.64470.13680.06830.569-0.5436-0.202-0.6066-0.50910.24450.18830.7141-0.01680.08830.2613-0.05840.438683.3245-11.3721-9.9276
36.3335-0.51250.63746.3126-0.97295.14510.0467-0.4663-0.3287-0.2533-0.0507-1.05070.71170.5197-0.03190.5740.0539-0.02720.3254-0.0110.458187.8795-20.3756-5.0178
42.38381.14-0.2574.3962-0.24812.32680.0278-0.04280.3469-0.4274-0.03580.3531-0.4142-0.2357-0.00980.66670.1046-0.06210.2688-0.06830.351768.9612-14.7449-9.6436
54.66491.09480.4978.4599-0.53417.56690.3823-0.27870.46950.388-0.39270.4918-0.1383-0.34710.06490.4028-0.0020.00970.311-0.03620.320960.2209-21.1766-0.4581
66.9604-1.32311.31528.0876-0.95855.97880.322-0.715-0.40840.5759-0.24610.49290.0694-0.3991-0.01710.5148-0.08830.03930.3606-0.0030.352562.6449-26.24885.7651
76.63363.18880.31296.45370.54825.8012-0.05440.0149-0.3018-0.9756-0.08960.92250.7497-0.61050.1590.649-0.0755-0.15260.387-0.06270.524256.8459-33.3859-8.9232
83.92366.1445-0.49719.6271-0.86132.094-0.96181.019-0.7192-1.44121.2957-0.00780.1963-0.6284-0.35660.9012-0.2071-0.21670.6509-0.00380.648558.7207-26.5596-17.113
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 166 )
2X-RAY DIFFRACTION2chain 'A' and (resid 167 through 185 )
3X-RAY DIFFRACTION3chain 'A' and (resid 186 through 207 )
4X-RAY DIFFRACTION4chain 'A' and (resid 208 through 296 )
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 319 )
6X-RAY DIFFRACTION6chain 'A' and (resid 320 through 354 )
7X-RAY DIFFRACTION7chain 'A' and (resid 355 through 394 )
8X-RAY DIFFRACTION8chain 'A' and (resid 395 through 408 )

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