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- PDB-4u9u: Crystal structure of NqrF FAD-binding domain from Vibrio cholerae -

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Basic information

Entry
Database: PDB / ID: 4u9u
TitleCrystal structure of NqrF FAD-binding domain from Vibrio cholerae
ComponentsNa(+)-translocating NADH-quinone reductase subunit F
KeywordsOXIDOREDUCTASE / sodium translocation
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 / flavin adenine dinucleotide 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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Na(+)-translocating NADH-quinone reductase subunit F
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.55 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 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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
B: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,81610
Polymers64,0322
Non-polymers1,7848
Water9,080504
1
A: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9085
Polymers32,0161
Non-polymers8924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na(+)-translocating NADH-quinone reductase subunit F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9085
Polymers32,0161
Non-polymers8924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.430, 89.070, 90.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 32016.178 Da / Num. of mol.: 2 / Fragment: UNP residues 130-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: nqrF, VC_2290 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9X4Q8, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor

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Non-polymers , 5 types, 512 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2.31 Å3/Da / Density % sol: 46.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 35% PEG4000, 0.1M citric acid NaOH, pH5, 0.2M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0, 1.07152, 1.07208, 1.0628
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 30, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.071521
31.072081
41.06281
ReflectionNumber: 268967 / Rmerge(I) obs: 0.078 / Χ2: 1.13 / D res high: 2.1 Å / Num. obs: 50061 / % possible obs: 75.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
104561310.028
610221310.037
46673010.044
341309710.072
2.531522310.186
2.32.5639310.366
2.22.3308910.463
2.12.2270310.626
ReflectionResolution: 1.55→45 Å / Num. obs: 86120 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 22.3 % / Biso Wilson estimate: 26.64 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.109 / Rrim(I) all: 0.111 / Χ2: 1.068 / Net I/σ(I): 16.51 / Num. measured all: 1925204
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.55-1.650.4962.9870.9625453614686144533.07698.4
1.65-1.70.7831.8681.98145538604459841.90799
1.7-1.80.8921.2313.3224118510261101751.25799.2
1.8-1.90.9670.6946.28194160821881550.70999.2
1.9-20.9890.39510.74161691666666360.40399.5
2-30.9980.13824.6966774028402283490.14199.8
3-40.9990.07442.42150859703770360.076100
4-50.9990.0645.6553225254625440.06199.9
5-60.9990.05645.6923931114311410.05799.8
6-100.9990.05344.4925243127212700.05499.8
10-450.9990.05343.9270963873770.05497.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
XDSdata reduction
SOLVEphasing
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
Cootmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
XSCALEdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.55→40 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1964 4301 4.99 %
Rwork0.1618 81810 -
obs0.1635 86111 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.98 Å2 / Biso mean: 32.7921 Å2 / Biso min: 14.9 Å2
Refinement stepCycle: final / Resolution: 1.55→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4476 0 118 504 5098
Biso mean--24.97 42.42 -
Num. residues----557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154825
X-RAY DIFFRACTIONf_angle_d1.4196569
X-RAY DIFFRACTIONf_chiral_restr0.083646
X-RAY DIFFRACTIONf_plane_restr0.01853
X-RAY DIFFRACTIONf_dihedral_angle_d16.0461787
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.56760.41241470.46272670281798
1.5676-1.5860.45691460.39412621276798
1.586-1.60540.37611420.38842691283399
1.6054-1.62570.30341350.30872675281099
1.6257-1.64710.32981380.30632692283098
1.6471-1.66970.32551270.28562689281699
1.6697-1.69350.28431320.26112700283299
1.6935-1.71880.24681350.24372702283799
1.7188-1.74560.29441540.22542687284199
1.7456-1.77430.25331490.22572675282499
1.7743-1.80490.25041430.18812690283399
1.8049-1.83770.21461440.18842720286499
1.8377-1.8730.21981400.18672675281599
1.873-1.91130.22341420.19262696283899
1.9113-1.95280.23531450.18842748289399
1.9528-1.99820.22021420.192693283599
1.9982-2.04820.20081450.172727432888100
2.0482-2.10360.20941410.1612716285799
2.1036-2.16550.20051440.155827142858100
2.1655-2.23540.16591430.155327312874100
2.2354-2.31530.21291440.155727382882100
2.3153-2.40790.20471450.166227492894100
2.4079-2.51750.19591440.170327402884100
2.5175-2.65020.23211460.166227552901100
2.6502-2.81620.17031460.17527662912100
2.8162-3.03360.21261450.16927682913100
3.0336-3.33870.19781460.154127902936100
3.3387-3.82150.16281470.131627882935100
3.8215-4.81340.14961490.112528312980100
4.8134-39.97030.16881550.136129573112100
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)
10.91660.2761-0.15240.25530.31090.45210.01980.2985-0.1621-0.0974-0.0171-0.0974-0.0943-0.06770.00190.23070.00760.01640.2681-0.03340.201622.195139.429612.2186
20.2197-0.3205-0.00460.4354-0.07770.0860.26880.1610.1155-0.0615-0.16460.0373-0.133-0.038-00.25050.01410.02730.2625-0.00930.203822.695249.841113.289
30.89840.48620.05061.65870.12450.24220.06390.099-0.18330.119-0.06880.10090.01970.0432-0.02340.1997-0.00090.02360.1878-0.03970.215116.142733.28719.3911
40.6457-0.091-0.54720.828-0.36820.42090.13010.0640.01410.1447-0.06670.0188-0.1064-0.0490.01030.2286-0.00570.02860.1781-0.03190.160423.245445.017318.8635
51.1495-0.47940.63850.5845-0.20670.69140.050.2403-0.31530.02330.0141-0.1088-0.06190.27450.01670.1957-0.0142-0.00480.2564-0.04210.28137.96835.004625.0537
60.60940.2036-0.3630.6476-0.3290.7692-0.108-0.3588-0.00450.32910.03190.0124-0.2164-0.0459-00.3618-0.021-0.03340.3603-0.01160.22535.136841.493238.6014
71.0933-0.1870.4450.75480.31360.24430.14560.0919-0.1443-0.2159-0.0906-0.11640.17520.1666-00.29210.0133-0.0190.19670.01710.224533.928626.1368-21.5521
80.33070.0372-0.17970.37090.29670.58950.1095-0.0389-0.1536-0.0473-0.02060.0220.2388-0.21860.1070.2551-0.0846-0.0850.23920.08150.258321.905922.6772-16.0101
91.31870.40370.8091.12640.24361.04240.2726-0.2855-0.1790.09070.00330.01260.3125-0.33950.43120.2479-0.0842-0.07850.28160.11550.235224.995624.617-10.7807
101.0940.44160.37140.27060.13541.29120.1548-0.03940.0237-0.0372-0.05120.01750.052-0.14020.01230.213-0.0089-0.00120.20060.03910.21528.289831.3148-15.2081
110.15-0.08150.18330.19890.18240.74820.11870.0676-0.0121-0.0210.0052-0.06110.00540.0788-00.1907-0.00780.02250.18180.00830.206544.76738.5706-11.431
120.09520.00790.20650.2614-0.12770.28080.1139-0.0938-0.39340.0829-0.0428-0.15880.29430.094300.23020.0065-0.02460.25770.04910.284943.034628.4315-3.7125
130.9206-0.40880.36640.17760.35211.32740.1402-0.37210.02140.13360.0388-0.0306-0.08220.19060.01470.2236-0.01340.00720.260.02450.222343.074838.59563.7778
140.0904-0.1961-0.15760.2840.37560.5470.0698-0.0578-0.01-0.23380.0899-0.2083-0.2831-0.21820.05980.27650.02810.06730.1911-0.00830.240636.490548.583-4.2592
150.5889-0.411-0.91240.69410.79051.55490.13130.32590.3407-0.5387-0.40380.4932-1.1094-1.0944-0.15210.57110.11390.02330.04990.09950.283134.606149.8246-10.4512
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 130 through 153 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 154 through 174 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 175 through 243 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 244 through 275 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 276 through 354 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 355 through 408 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 130 through 166 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 167 through 185 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 186 through 222 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 223 through 275 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 276 through 311 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 312 through 329 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 330 through 369 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 370 through 394 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 395 through 407 )B0

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