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- PDB-5k1s: crystal structure of AibC -

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Basic information

Entry
Database: PDB / ID: 5k1s
Titlecrystal structure of AibC
ComponentsOxidoreductase, zinc-binding dehydrogenase family
KeywordsOXIDOREDUCTASE / medium chain reductase / isovalerate / hexahistidine tag / TEV-protease recognition sequence
Function / homology
Function and homology information


oxidoreductase activity / zinc ion binding
Similarity search - Function
Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase ...Quinone oxidoreductase/zeta-crystallin, conserved site / Quinone oxidoreductase / zeta-crystallin signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Oxidoreductase, zinc-binding dehydrogenase family
Similarity search - Component
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.55 Å
AuthorsBock, T. / Mueller, R. / Blankenfeldt, W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2016
Title: Crystal structure of AibC, a reductase involved in alternative de novo isovaleryl coenzyme A biosynthesis in Myxococcus xanthus.
Authors: Bock, T. / Muller, R. / Blankenfeldt, W.
History
DepositionMay 18, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, zinc-binding dehydrogenase family
C: Oxidoreductase, zinc-binding dehydrogenase family
B: Oxidoreductase, zinc-binding dehydrogenase family
D: Oxidoreductase, zinc-binding dehydrogenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,43412
Polymers152,9114
Non-polymers5238
Water1,928107
1
A: Oxidoreductase, zinc-binding dehydrogenase family
B: Oxidoreductase, zinc-binding dehydrogenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7176
Polymers76,4552
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-86 kcal/mol
Surface area27550 Å2
MethodPISA
2
C: Oxidoreductase, zinc-binding dehydrogenase family
D: Oxidoreductase, zinc-binding dehydrogenase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,7176
Polymers76,4552
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-50 kcal/mol
Surface area27010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.294, 77.427, 309.638
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Oxidoreductase, zinc-binding dehydrogenase family /


Mass: 38227.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (strain DK 1622) (bacteria)
Strain: DK 1622 / Gene: MXAN_4266 / Plasmid: pET19m / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D4I2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 3 M NaCl, 0.1 M HEPES pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1.2779 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2779 Å / Relative weight: 1
ReflectionResolution: 2.55→48.36 Å / Num. obs: 61786 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 53.71 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.042 / Rrim(I) all: 0.152 / Net I/σ(I): 16.6 / Num. measured all: 800735
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.55-2.6213.61.5841100
11.4-48.3611.60.05198.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.5.25data scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.55→42.942 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 27.24
RfactorNum. reflection% reflection
Rfree0.2688 3087 5 %
Rwork0.2343 --
obs0.236 61690 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 291.05 Å2 / Biso mean: 82.6892 Å2 / Biso min: 25.92 Å2
Refinement stepCycle: final / Resolution: 2.55→42.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9836 0 8 107 9951
Biso mean--91.17 37.86 -
Num. residues----1382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0029992
X-RAY DIFFRACTIONf_angle_d0.43713598
X-RAY DIFFRACTIONf_chiral_restr0.0421624
X-RAY DIFFRACTIONf_plane_restr0.0021802
X-RAY DIFFRACTIONf_dihedral_angle_d12.1895940
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 22 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.55-2.58990.37321460.350326192765
2.5899-2.63230.37081670.333925782745
2.6323-2.67770.34921440.322526232767
2.6777-2.72640.32761420.308426132755
2.7264-2.77880.31491460.308426312777
2.7788-2.83550.32411590.297826062765
2.8355-2.89720.28811270.303926242751
2.8972-2.96460.36841240.303826712795
2.9646-3.03870.33721510.308126432794
3.0387-3.12080.31421380.288325942732
3.1208-3.21260.29541510.269126652816
3.2126-3.31630.29571410.26126522793
3.3163-3.43480.3131350.244426112746
3.4348-3.57220.28861720.243626132785
3.5722-3.73470.26381530.224226492802
3.7347-3.93150.23941140.221327162830
3.9315-4.17760.25021340.19826482782
4.1776-4.49990.1761230.181827292852
4.4999-4.95210.19841480.180126862834
4.9521-5.66730.241300.203427122842
5.6673-7.13490.25551320.228427842916
7.1349-42.94810.27221100.211129363046
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)
11.11130.06940.430.2548-0.12330.24080.1581-0.086-0.27190.11060.0803-0.03430.0447-0.2651-0.1050.3217-0.0273-0.04270.9330.22890.545730.769312.5488160.8677
22.0563-0.0141-0.34160.8592-0.13730.44320.0863-0.1053-0.04220.0154-0.02360.02770.00450.0959-0.00460.2473-0.0153-0.00380.79050.15310.477218.116121.7177158.1853
30.5759-0.52420.23490.86020.07440.37180.2799-0.17580.254-0.2594-0.2291-0.3292-0.28180.3583-0.04110.3155-0.00650.12970.69710.10070.537223.924532.8499150.568
43.0116-0.05521.09152.2471.12890.98150.0956-0.18670.00450.2118-0.054-0.01530.0232-0.0729-0.00180.93220.20260.05370.6893-0.07420.77489.970151.8914160.768
53.1584-0.10992.38360.84840.32421.99080.0535-0.06720.20320.1514-0.03230.1187-0.2427-0.16950.02030.86340.23230.20010.743-0.19010.69952.71954.5814157.1506
60.7434-0.24440.12740.6125-0.13110.58480.0887-0.35950.26440.0444-0.088-0.1307-0.6482-0.2780.02360.53140.17720.15770.7050.07360.56818.789644.2599147.9847
72.60531.4076-0.4021.37880.22641.63330.0245-0.17550.36330.3516-0.03470.2203-0.2507-0.12670.02710.446-0.07160.09591.10560.04670.533717.515128.8067169.744
80.458-0.3690.05313.6345-0.13450.01240.1603-0.0752-0.0317-0.01980.10430.17190.21820.0328-0.05881.0264-0.1003-0.24630.42650.03670.4203-7.345154.540470.655
90.24160.01510.02820.67520.63950.62650.06350.15670.2007-0.0790.02970.1825-0.08970.0085-0.06211.08590.0075-0.09290.31010.05480.3979-0.254148.470772.0156
100.4486-0.30620.23550.4055-0.06620.6062-0.085-0.09070.1031-0.32410.10980.0115-0.08670.175-0.05460.8543-0.0104-0.05960.2965-0.02110.47736.019245.120480.6527
111.7442-0.3223-0.51840.85840.04880.6743-0.0834-0.22210.11340.0734-0.0572-0.258-0.10410.39250.06360.54680.0296-0.02420.6165-0.05010.66125.097738.511289.253
121.7104-0.2497-0.24481.7726-0.58930.2593-0.07970.25460.0365-0.21190.0868-0.36870.05690.2689-0.04080.54380.08090.07960.8027-0.05150.567130.601133.652177.3644
130.3763-0.185-0.02760.4609-0.20390.3167-0.1163-0.0098-0.0107-0.36740.1056-0.40840.54330.6244-0.00620.85280.27920.05870.7004-0.09520.627226.813623.403886.7849
141.6718-0.1237-0.44330.68860.31391.6853-0.07850.1932-0.0654-0.1839-0.0512-0.3388-0.09930.3812-0.01140.8812-0.08710.05450.55160.01270.630521.422246.773477.8738
151.36890.36830.15283.1725-0.27341.7745-0.08730.333-0.2781-0.10550.0188-0.33930.24530.39150.03821.21140.00230.06580.511-0.0360.409410.381437.447563.4176
160.7602-0.21840.11871.1321-0.36920.5321-0.1253-0.09240.04420.0485-0.0264-0.0620.0069-0.0027-0.01361.1940.91550.1461.18560.21180.9826-21.73166.2188120.2583
170.5799-0.74140.02511.20.10710.13980.09160.03370.2957-0.1790.17110.0421-0.844-0.40010.30711.16820.91020.23350.87420.3710.77-4.697155.7793119.5354
180.43930.1288-0.16960.9392-0.14791.18490.1755-0.0573-0.1125-0.2118-0.00690.35180.1044-0.5815-0.07420.50840.2531-0.01040.95630.18580.651-3.204729.493125.912
190.06110.08760.03840.3532-0.30010.65130.28420.02510.0068-0.38930.03610.254-0.4166-0.31220.00250.62340.44030.15270.69690.19780.58250.59842.8094128.3803
200.9551-0.06590.370.0055-0.01990.15720.0236-0.0229-0.2771-0.0668-0.08530.27250.3353-0.11940.10971.04710.4864-0.10781.15530.2270.9728-22.898549.1113116.3865
210.00290.0001-0.00380.001-0.00120.0034-0.0565-0.1459-0.21520.1966-0.03160.25790.3604-0.39760.09781.28580.31060.20261.4409-0.00971.5987-19.607343.0373118.8829
224.00580.23560.02355.7616-3.20927.9444-0.01450.26650.1819-0.326-0.1277-0.0901-0.01660.10030.091.24670.3158-0.07391.29410.2721.2299-20.23457.9269109.0343
230.9051-0.44820.28620.4897-0.31010.40310.0742-0.1771-0.15260.04550.0605-0.22970.69960.63740.04040.82770.6529-0.24380.936-0.04220.689330.736712.6608115.4902
240.56850.01240.68460.4489-0.28761.46340.0329-0.1968-0.3126-0.18980.147-0.04130.47740.1953-0.1030.80740.2607-0.11760.4698-0.04530.577715.75219.7044104.5233
250.7343-0.19410.08081.26110.38851.72050.13390.1156-0.3999-0.2871-0.25450.32430.1264-0.2344-0.06311.24550.6471-0.32010.8231-0.11521.05825.9871-2.6388117.0956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -13 through 28 )A-13 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 62 )A29 - 62
3X-RAY DIFFRACTION3chain 'A' and (resid 63 through 190 )A63 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 209 )A191 - 209
5X-RAY DIFFRACTION5chain 'A' and (resid 210 through 230 )A210 - 230
6X-RAY DIFFRACTION6chain 'A' and (resid 231 through 312 )A231 - 312
7X-RAY DIFFRACTION7chain 'A' and (resid 313 through 344 )A313 - 344
8X-RAY DIFFRACTION8chain 'C' and (resid -13 through 11 )C-13 - 11
9X-RAY DIFFRACTION9chain 'C' and (resid 12 through 40 )C12 - 40
10X-RAY DIFFRACTION10chain 'C' and (resid 41 through 150 )C41 - 150
11X-RAY DIFFRACTION11chain 'C' and (resid 151 through 168 )C151 - 168
12X-RAY DIFFRACTION12chain 'C' and (resid 169 through 213 )C169 - 213
13X-RAY DIFFRACTION13chain 'C' and (resid 214 through 293 )C214 - 293
14X-RAY DIFFRACTION14chain 'C' and (resid 294 through 315 )C294 - 315
15X-RAY DIFFRACTION15chain 'C' and (resid 316 through 344 )C316 - 344
16X-RAY DIFFRACTION16chain 'B' and (resid 0 through 28 )B0 - 28
17X-RAY DIFFRACTION17chain 'B' and (resid 29 through 189 )B29 - 189
18X-RAY DIFFRACTION18chain 'B' and (resid 190 through 253 )B190 - 253
19X-RAY DIFFRACTION19chain 'B' and (resid 254 through 311 )B254 - 311
20X-RAY DIFFRACTION20chain 'B' and (resid 312 through 330 )B312 - 330
21X-RAY DIFFRACTION21chain 'B' and (resid 331 through 338 )B331 - 338
22X-RAY DIFFRACTION22chain 'B' and (resid 339 through 344 )B339 - 344
23X-RAY DIFFRACTION23chain 'D' and (resid -1 through 217 )D-1 - 217
24X-RAY DIFFRACTION24chain 'D' and (resid 218 through 312 )D218 - 312
25X-RAY DIFFRACTION25chain 'D' and (resid 313 through 343 )D313 - 343

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