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- PDB-4xhf: Crystal structure of Shewanella oneidensis NqrC -

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Basic information

Entry
Database: PDB / ID: 4xhf
TitleCrystal structure of Shewanella oneidensis NqrC
ComponentsNa-translocating NADH-quinone reductase subunit C NqrC
KeywordsOXIDOREDUCTASE / FMN / COVALENT FLAVINYLATION
Function / homology
Function and homology information


plasma membrane ATP synthesis coupled electron transport / NADH:ubiquinone reductase (Na+-transporting) / sodium ion transport / NADH dehydrogenase (ubiquinone) activity / FMN binding / membrane => GO:0016020 / plasma membrane
Similarity search - Function
Na(+)-translocating NADH-quinone reductase subunit C / FMN-binding / FMN-binding domain / FMN_bind
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Na(+)-translocating NADH-quinone reductase subunit C
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.76 Å
AuthorsTomchick, D.R. / Brautigam, C.A. / Deka, R.K. / Norgard, M.V.
CitationJournal: Microbiologyopen / Year: 2016
Title: Molecular insights into the enzymatic diversity of flavin-trafficking protein (Ftp; formerly ApbE) in flavoprotein biogenesis in the bacterial periplasm.
Authors: Deka, R.K. / Brautigam, C.A. / Liu, W.Z. / Tomchick, D.R. / Norgard, M.V.
History
DepositionJan 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2016Group: Database references

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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 C NqrC
B: Na-translocating NADH-quinone reductase subunit C NqrC
C: Na-translocating NADH-quinone reductase subunit C NqrC
D: Na-translocating NADH-quinone reductase subunit C NqrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0369
Polymers116,1884
Non-polymers1,8485
Water11,728651
1
A: Na-translocating NADH-quinone reductase subunit C NqrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5032
Polymers29,0471
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Na-translocating NADH-quinone reductase subunit C NqrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5032
Polymers29,0471
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Na-translocating NADH-quinone reductase subunit C NqrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5032
Polymers29,0471
Non-polymers4561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Na-translocating NADH-quinone reductase subunit C NqrC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5263
Polymers29,0471
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.914, 93.476, 71.139
Angle α, β, γ (deg.)90.000, 100.240, 90.000
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer. There are 4 biological units in the asymmetric unit.

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Components

#1: Protein
Na-translocating NADH-quinone reductase subunit C NqrC


Mass: 29046.902 Da / Num. of mol.: 4 / Fragment: Soluble fragment, UNP residues 33-264
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Gene: nqrC, SO_0904 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8EID8, Oxidoreductases; Acting on NADH or NADPH; With a quinone or similar compound as acceptor
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 651 / 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

Crystal
IDDensity Matthews3/Da)Density % sol (%)
1238.41
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop50.1 M MIB (malonate, imidazole and boric acid), 25% (w/v) PEG 1,500
2932vapor diffusion, hanging drop90.1 M bicine, 0.1 M NaCl, 27% (w/v) PEG 1,500, 20% (v/v) ethylene glycol

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
32
42
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.97918
SYNCHROTRONAPS 19-ID20.97918
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 7, 2014 / Details: monochromator
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
21
Reflection twinOperator: l,-k,h / Fraction: 0.38
ReflectionResolution: 1.76→50 Å / Num. all: 89381 / Num. obs: 89381 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.036 / Rrim(I) all: 0.075 / Χ2: 0.855 / Net I/av σ(I): 15.927 / Net I/σ(I): 14.4 / Num. measured all: 370660
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.793.40.38443190.7480.2410.4560.66496.3
1.79-1.823.60.34344130.8120.210.4040.6898.1
1.82-1.8640.28544460.8950.1620.3280.73498.4
1.86-1.94.20.22944180.9240.1270.2620.76798.7
1.9-1.944.20.244420.9430.110.2290.86598.5
1.94-1.984.20.16544610.9570.0910.1890.87298.9
1.98-2.034.20.14444470.9640.080.1650.87398.9
2.03-2.094.20.13344300.9680.0730.1520.95299
2.09-2.154.20.11644660.9760.0640.1330.91799
2.15-2.224.30.10244820.980.0570.1170.93999.2
2.22-2.34.30.09744960.9820.0530.1110.97799.2
2.3-2.394.30.08944590.9820.050.1020.93399.3
2.39-2.54.30.08344790.9820.0460.0950.89399.4
2.5-2.634.30.07844910.9860.0430.0890.90899.6
2.63-2.794.30.07344740.9870.0410.0840.90399.6
2.79-3.014.30.06945390.9890.0390.0790.90899.7
3.01-3.314.30.06544790.9910.0360.0750.92499.8
3.31-3.794.20.05945750.9950.0330.0670.90199.9
3.79-4.784.10.05145340.9960.0290.0590.7699.9
4.78-504.20.04445310.9980.0250.050.62397.7

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.76→33.713 Å / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 27.7 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2016 2032 2.29 %random selection
Rwork0.1657 86864 --
obs0.1684 88913 98.32 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.5 Å2 / Biso mean: 23.853 Å2 / Biso min: 6.06 Å2
Refinement stepCycle: final / Resolution: 1.76→33.713 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6917 0 197 651 7765
Biso mean--27.8 22.46 -
Num. residues----884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0047243
X-RAY DIFFRACTIONf_angle_d0.6489785
X-RAY DIFFRACTIONf_chiral_restr0.0261043
X-RAY DIFFRACTIONf_plane_restr0.0021249
X-RAY DIFFRACTIONf_dihedral_angle_d12.0312661
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 (%)
1.7606-1.80460.24821320.23515722585489
1.8046-1.85330.26031410.22526128626996
1.8533-1.90780.23351390.21016200633996
1.9078-1.96940.24741400.20176212635296
1.9694-2.03970.24111470.19176201634897
2.0397-2.12130.22211420.18716203634597
2.1213-2.21780.22851470.17896255640297
2.2178-2.33460.19481410.17676222636397
2.3346-2.48070.16531430.17566219636297
2.4807-2.67190.21411460.17136307645397
2.6719-2.94030.19541440.17076295643997
2.9403-3.36450.20381440.15536293643798
3.3645-4.2340.17911470.13296317646498
4.234-22.16830.1841520.1446290644296
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.63532.1691-1.26591.9106-1.06661.58570.07680.0393-0.33970.057-0.00750.1240.3422-0.1038-0.00450.2148-0.0105-0.02180.09390.02460.2015-1.6243-5.657845.9358
22.2923-0.86150.00091.46430.32421.1975-0.1895-0.26820.05410.17140.1474-0.11180.12910.08110.0390.11390.03020.00770.13160.00280.11045.98193.394247.2614
31.09650.1750.42210.9965-0.22821.69190.0237-0.07530.01560.17010.07240.2733-0.0105-0.2794-0.04170.193-0.00320.01440.1595-0.01740.2204-12.78766.855242.5089
42.75-0.3995-0.28592.03530.6972.7340.09410.1104-0.1596-0.1529-0.24720.1618-0.1556-0.43360.06410.12220.0376-0.02980.147-0.03660.205-15.52048.03828.4282
51.41540.61310.27241.83510.81192.0450.0321-0.1542-0.03380.0571-0.047-0.0404-0.02250.0172-0.02220.07130.0113-0.00170.07-0.0230.09271.85149.35839.9063
60.99080.1682-0.47220.76890.09911.3945-0.0513-0.1372-0.1318-0.106-0.00640.00740.10570.04980.02730.0990.0210.01270.0887-0.00630.14352.5069-0.00628.1338
75.0999-1.79230.00754.65210.29131.9240.37530.14510.1632-0.39220.0120.2736-0.39780.1604-0.18210.1965-0.00050.04560.1521-0.00510.1964.706115.595423.3762
80.95651.71930.06823.18830.37760.6366-0.04140.4613-0.1797-0.13290.08310.10710.0183-0.0586-0.0280.2053-0.02040.03520.2228-0.05070.21329.21945.076416.9727
91.4166-0.8386-0.76183.14551.14370.98140.03970.28440.0439-0.3775-0.1215-0.06-0.1199-0.08660.05750.13480.0109-0.00550.15090.01850.1695-3.41264.549621.7738
101.1753-0.12250.59670.49290.84423.9453-0.0529-0.00510.4997-0.165-0.06680.1599-0.47460.11860.0360.16150.0095-0.02270.1049-0.020.277-4.000118.434734.1849
114.13643.1975-2.22623.1304-2.01321.3893-0.02270.0887-0.50060.06290.1122-0.04030.2232-0.238-0.09320.2191-0.0258-0.03480.17840.02520.236627.4407-5.820781.5507
121.3910.4360.49981.32710.12762.0763-0.0318-0.0807-0.05170.11010.0467-0.12820.14660.1718-0.01560.1483-0.006-0.00980.1277-0.01470.151935.64744.606182.369
131.2094-0.0960.41370.5480.17442.7511-0.0737-0.1057-0.02870.0899-0.06750.0819-0.0584-0.36820.11980.18760.01790.00210.1848-0.04170.211515.45246.935772.0594
141.69570.66170.6891.67051.13722.6854-0.0271-0.1058-0.0059-0.0005-0.03220.036-0.11540.12920.09550.14580.01220.00920.1004-0.00820.104731.159110.238675.0623
151.10810.6081-0.08281.29130.20661.46680.08060.017-0.068-0.0331-0.0398-0.0645-0.07440.0428-0.05890.15890.0359-0.01370.1301-0.02460.11330.55155.970365.7789
160.96240.83210.28042.21720.4681.81130.1610.1428-0.08320.0277-0.08670.02450.07910.3291-0.05530.13030.0264-0.00420.169-0.03940.144733.89492.943461.2488
170.1980.45060.01321.5684-0.40260.35790.03830.25470.0014-0.36880.0772-0.0671-0.08980.1264-0.08050.1767-0.00540.01060.2117-0.02930.155732.68554.479154.7384
180.6467-0.3729-1.09011.33061.0472.314-0.15320.0660.4734-0.2011-0.1525-0.012-0.7363-0.11630.21310.2430.0338-0.08820.12590.00290.269924.478318.140168.2367
192.1124-0.63670.09922.33650.33811.67860.03880.1950.5495-0.01960.16050.026-0.4044-0.2013-0.08790.19810.02240.00260.14530.05980.2119-18.984430.65956.4881
201.7841-0.07610.74951.9337-0.61523.10270.10360.06250.1432-0.09160.05420.24840.1121-0.3747-0.14130.0966-0.00360.03360.16660.01410.1616-23.709622.724158.4371
211.39720.36190.6921.4970.86220.86760.0635-0.26950.25460.0849-0.15080.2144-0.0416-0.25780.02890.24120.00760.04280.2403-0.01090.2614-20.80121.998374.7129
224.3746-0.0186-0.35461.36780.26262.1754-0.0144-0.18580.04930.1610.0380.01420.1190.0235-0.02840.1769-0.044-0.0060.1859-0.00550.1051-7.474721.14179.9611
231.90290.65580.43091.13750.84131.80310.0290.101-0.02290.0003-0.02690.06880.046-0.15840.00950.0953-0.0054-0.00130.1030.02080.1148-15.803218.850560.8651
241.58460.0765-0.00831.40490.15910.87330.00050.11990.24340.0080.00810.0675-0.0771-0.0616-0.03220.1069-0.0199-0.0010.08810.01620.1411-4.153428.100961.615
252.43820.9965-1.13963.8432-0.38343.95630.13010.0636-0.15990.0379-0.0113-0.1670.22660.1545-0.1280.1194-0.0125-0.00450.1268-0.02130.15430.820812.753561.3836
260.42490.29180.34475.38822.36551.14280.19230.0573-0.0248-0.18920.0659-0.6179-0.16790.0813-0.14650.1609-0.0170.02030.1602-0.02550.27898.129523.002657.579
271.54881.7701-1.11363.444-1.45910.8139-0.0496-0.4687-0.2299-0.2018-0.242-0.44190.08670.26580.16670.10430.0090.02180.14330.03230.1411.493224.709969.0862
282.20220.6720.76750.87330.56461.79130.30570.0382-0.44860.12910.07650.07170.706-0.0825-0.27270.2839-0.0265-0.05640.13230.01920.1864-10.963110.122868.0572
292.3927-1.0231-0.46993.74111.21832.4549-0.2116-0.2760.61640.24430.04590.1976-0.4596-0.0920.16660.25350.0391-0.03950.206-0.02470.291521.491931.906525.5195
301.63630.9488-0.06531.10140.19991.89010.0563-0.01860.23840.0635-0.09320.1602-0.0937-0.23150.0530.12760.00410.00670.1708-0.00110.205919.595323.279729.2621
311.5260.73380.11790.92970.4431.6320.1619-0.22170.05330.1867-0.17580.00380.1178-0.16890.00420.1244-0.0362-0.00060.12250.00490.103828.498320.185435.196
320.9780.10620.35211.12830.73450.5387-0.0034-0.04230.0644-0.0765-0.09720.1035-0.064-0.02880.05520.1022-0.02730.0020.09710.01840.110636.459629.075327.0908
332.35750.1381-0.69694.9976-1.58915.32710.2898-0.2093-0.33850.2323-0.1494-0.0446-0.09340.526-0.12520.1109-0.0318-0.02410.13090.01850.171542.357913.845926.4005
340.5072-0.03690.1491.7190.53440.45260.0388-0.031-0.093-0.09250.0952-0.3575-0.03450.0466-0.12660.1096-0.00920.01420.1206-0.00170.157446.039524.875728.2571
352.5930.52490.13960.48180.93862.16580.13220.0481-0.51540.3504-0.0687-0.20960.4068-0.1644-0.11460.2005-0.0138-0.0290.12920.04150.180930.77910.077732.5562
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 52 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 77 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 102 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 103 through 119 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 120 through 143 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 144 through 189 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 203 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 204 through 224 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 225 through 238 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 239 through 254 )A0
11X-RAY DIFFRACTION11chain 'B' and (resid -3 through 52 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 53 through 77 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 78 through 119 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 120 through 143 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 144 through 163 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 164 through 203 )B0
17X-RAY DIFFRACTION17chain 'B' and (resid 204 through 238 )B0
18X-RAY DIFFRACTION18chain 'B' and (resid 239 through 253 )B0
19X-RAY DIFFRACTION19chain 'C' and (resid 38 through 61 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 62 through 77 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 78 through 102 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 103 through 119 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 120 through 143 )C0
24X-RAY DIFFRACTION24chain 'C' and (resid 144 through 189 )C0
25X-RAY DIFFRACTION25chain 'C' and (resid 190 through 203 )C0
26X-RAY DIFFRACTION26chain 'C' and (resid 204 through 224 )C0
27X-RAY DIFFRACTION27chain 'C' and (resid 225 through 238 )C0
28X-RAY DIFFRACTION28chain 'C' and (resid 239 through 254 )C0
29X-RAY DIFFRACTION29chain 'D' and (resid 37 through 53 )D0
30X-RAY DIFFRACTION30chain 'D' and (resid 54 through 99 )D0
31X-RAY DIFFRACTION31chain 'D' and (resid 100 through 143 )D0
32X-RAY DIFFRACTION32chain 'D' and (resid 144 through 189 )D0
33X-RAY DIFFRACTION33chain 'D' and (resid 190 through 203 )D0
34X-RAY DIFFRACTION34chain 'D' and (resid 204 through 238 )D0
35X-RAY DIFFRACTION35chain 'D' and (resid 239 through 255 )D0

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Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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