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- PDB-4o5m: X-ray Crystal Structure of Isovaleryl-CoA Dehydrogenase from Bruc... -

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Basic information

Entry
Database: PDB / ID: 4o5m
TitleX-ray Crystal Structure of Isovaleryl-CoA Dehydrogenase from Brucella suis
ComponentsIsovaleryl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


isovaleryl-CoA dehydrogenase / isovaleryl-CoA dehydrogenase activity / flavin adenine dinucleotide binding / metal ion binding
Similarity search - Function
Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal ...Isovaleryl-CoA dehydrogenase / Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Butyryl-CoA Dehydrogenase, subunit A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A; domain 2 / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase/oxidase, N-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA dehydrogenase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal domain superfamily / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Isovaleryl-CoA dehydrogenase / Isovaleryl-CoA dehydrogenase
Similarity search - Component
Biological speciesBrucella suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: X-ray Crystal Structure of Isovaleryl-CoA Dehydrogenase from Brucella suis
Authors: Fairman, J.W. / Edwards, T.E. / Lorimer, D.
History
DepositionDec 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isovaleryl-CoA dehydrogenase
B: Isovaleryl-CoA dehydrogenase
C: Isovaleryl-CoA dehydrogenase
D: Isovaleryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,5648
Polymers169,9894
Non-polymers5754
Water4,486249
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14000 Å2
ΔGint-104 kcal/mol
Surface area48040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.210, 91.070, 102.140
Angle α, β, γ (deg.)90.000, 99.250, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein
Isovaleryl-CoA dehydrogenase /


Mass: 42497.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis (bacteria) / Strain: 1330 / Gene: ivd, BR0020, BS1330_I0020 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8G3C9, UniProt: A0A0H3G544*PLUS, isovaleryl-CoA dehydrogenase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Triethylene glycol dimethyl ether


Mass: 178.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.22 Å3/Da / Density % sol: 44.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.4 uL protein at 17.53 mg/ml + 0.4 uL JCSG+ D10 - 40% PEG 300, 0.2 M Calcium acetate, 0.1 sodium cacodylate, pH 6.50, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 75627 / Num. obs: 74678 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 40.03 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 26.87
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.260.5322.719461548698.5
2.26-2.320.4323.3219139538698.4
2.32-2.390.314.4618445517798.8
2.39-2.460.2465.7318043506998.7
2.46-2.540.2056.7817541491799
2.54-2.630.1738.1916928476499.1
2.63-2.730.12510.9816238458698.7
2.73-2.840.113.5515702443798.8
2.84-2.970.07417.8514844421799.1
2.97-3.110.05523.1514157407599.2
3.11-3.280.03831.313437387198.7
3.28-3.480.02840.3512568365199.2
3.48-3.720.02249.2611705345699.2
3.72-4.020.01760.7810680318998.6
4.02-4.40.01569.649696295499
4.4-4.920.01472.948707267698.7
4.92-5.680.01471.817460235097.9
5.68-6.960.01571.336617200498.3
6.96-9.840.01291.045291155298.4
9.840.01196.57278786195.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→46.282 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.813 / SU ML: 0.27 / σ(F): 1.35 / Phase error: 25.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 3752 5.03 %
Rwork0.2003 --
obs0.202 74661 98.75 %
all-75627 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.68 Å2 / Biso mean: 59.3933 Å2 / Biso min: 23.66 Å2
Refinement stepCycle: LAST / Resolution: 2.2→46.282 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10250 0 37 249 10536
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00310460
X-RAY DIFFRACTIONf_angle_d0.71314168
X-RAY DIFFRACTIONf_chiral_restr0.0271601
X-RAY DIFFRACTIONf_plane_restr0.0031865
X-RAY DIFFRACTIONf_dihedral_angle_d11.5023621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.22780.30941280.29412669279798
2.2278-2.25720.32311360.28292547268398
2.2572-2.28810.33051510.28262622277398
2.2881-2.32080.30621290.272632276198
2.3208-2.35540.29741170.24622619273699
2.3554-2.39220.32581370.2462584272199
2.3922-2.43140.27131440.23252622276699
2.4314-2.47330.25841490.23322601275099
2.4733-2.51830.27281350.22972609274499
2.5183-2.56670.23671470.23132624277199
2.5667-2.61910.27531470.222630277799
2.6191-2.67610.26411450.22542623276899
2.6761-2.73830.28471280.21972634276299
2.7383-2.80680.31321310.22932586271799
2.8068-2.88270.28611380.22352615275399
2.8827-2.96750.2521320.22872644277699
2.9675-3.06330.30551470.22442650279799
3.0633-3.17270.26151360.21762632276899
3.1727-3.29970.24081350.21182627276299
3.2997-3.44980.24821380.19932624276299
3.4498-3.63170.23211350.18462650278599
3.6317-3.85910.19151560.17712612276899
3.8591-4.15690.17211520.15842637278999
4.1569-4.57490.20761430.16162636277999
4.5749-5.23610.20191540.16822634278899
5.2361-6.59380.22411200.20692649276998
6.5938-46.2820.19581420.18292697283998
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)
14.15031.3768-0.30863.64570.4143.0214-0.093-0.3749-0.46520.05250.2109-0.159-0.04810.2211-0.11660.21190.0016-0.01730.52270.1090.417477.082322.44594.6452
23.7512-0.64950.30112.2464-0.93463.7513-0.0072-0.0535-1.3215-0.16290.31860.13190.47250.655-0.24020.320.1038-0.02110.6568-0.09110.962787.86016.457484.018
35.8218-3.4672-2.01133.6734-0.79313.82560.36510.5651-0.3657-0.3916-0.16270.3366-0.08270.409-0.19090.3159-0.00850.02080.8895-0.18720.725191.894213.585176.9262
45.1998-3.4451-3.60753.37251.69646.24780.50990.4205-0.5595-0.7368-0.27390.0247-0.61880.878-0.22380.17240.0097-0.0690.8871-0.18430.699890.69916.707577.7281
55.0671-2.9274-3.06022.97633.73945.5142-0.1607-0.1825-0.1171-0.23910.22770.0823-0.11350.147-0.03810.2318-0.0083-0.06220.39050.07310.319468.413530.231188.5122
64.06673.52723.29363.48422.0297.4639-0.6511-0.66830.0816-0.65570.5036-0.1135-1.80520.51690.15460.7337-0.0626-0.06640.56-0.050.465956.21249.491191.9243
71.74780.0268-0.33464.525-1.2391.68440.0274-0.0222-0.2051-0.1273-0.1706-0.0789-0.17050.02990.13450.250.005-0.05770.43470.07720.326767.164829.191883.1128
84.70195.55125.02138.22136.11535.38370.73890.5307-1.9226-0.14621.2475-0.40170.64640.0949-1.98591.08320.0833-0.20560.7950.12281.270161.920115.137767.7541
95.60982.81521.09411.9318-0.67843.5097-0.19670.32350.8229-0.0770.27150.8093-0.238-0.9429-0.10280.46230.1141-0.07490.75630.14730.871432.887849.092155.8643
101.9016-0.2345-0.24311.93530.15224.455-0.09560.7760.2119-0.64290.16690.4110.1177-0.8059-0.020.557-0.1152-0.1930.830.17890.612136.488141.239441.8223
113.35551.0778-0.15951.9605-0.24357.8816-0.14550.4631-0.4775-0.85790.32820.34051.1665-0.7371-0.23490.95-0.2601-0.15420.74840.060.668734.111227.398443.6026
124.65491.05660.24686.9388-0.41616.6561-0.0591-0.0776-0.3595-0.26950.094-1.38880.8010.65990.0060.7585-0.0095-0.06720.89490.02670.748244.604331.833333.5631
134.74771.5658-1.99583.379-0.92397.36050.0182-0.03960.3528-0.0160.25130.6271-0.207-0.5931-0.22810.26690.0399-0.03950.27620.10050.509545.299747.909864.9213
149.30575.9611-2.78613.9097-1.63061.0859-0.19080.62611.3522-2.53810.77960.63980.92880.5637-0.40991.1732-0.0459-0.18720.5439-0.01160.803557.81142.37247.109
153.17492.4298-3.13412.5257-2.90138.6193-0.0949-0.08030.2276-0.32340.19720.52810.0684-0.52560.01160.2782-0.0119-0.07710.35850.06120.497740.891137.564166.7408
164.25742.2361-6.09238.7887-2.20378.9113-0.12571.4156-0.5095-1.1646-0.22170.2011-0.2528-1.26680.22640.66240.1004-0.12580.5662-0.06020.400163.204634.209250.8373
175.314-4.33275.74483.6779-4.24577.44071.34390.8369-0.7613-2.5431-0.6382-0.11342.31810.5652-0.46080.9918-0.0497-0.1470.55730.02270.811951.688810.981675.9357
184.1984-0.1286-0.5251.3989-0.17231.89070.0249-0.469-0.53740.1077-0.02350.11560.1751-0.23230.01110.2335-0.0487-0.03310.5910.11650.518133.817714.201689.0995
194.3233-2.75142.14992.9857-3.68915.4238-0.7511-0.7150.29851.27090.09730.6538-0.87420.70420.35820.6491-0.20390.26511.0893-0.32530.683919.369936.7699104.2756
205.477-0.9073-2.24741.3608-0.54351.55660.0121-0.93440.34870.3358-0.0032-0.0307-0.25510.2783-0.00530.2946-0.073-0.00750.8748-0.03910.610923.686530.165593.9512
215.1585-3.9679-0.22993.17310.16880.00850.42-0.98131.00790.4617-0.01872.36980.3373-0.5979-0.45350.6082-0.13130.15190.947-0.03271.052341.060828.336796.7232
221.25610.04741.22661.61470.74694.4879-0.0605-0.0372-0.0788-0.23120.0042-0.0790.24230.17420.03910.21780.0102-0.0230.38190.06830.489250.95618.78576.403
232.05970.30941.93972.08980.53789.81350.0910.1294-0.0271-0.16840.0453-0.04820.04830.0861-0.10610.21580.05080.02480.46240.13520.519243.782826.381775.0859
244.14983.89836.37333.8396.00469.8148-0.108-0.79960.4490.41-0.80041.35150.3175-1.36020.94240.62840.02640.08780.83970.06140.858950.077838.136692.9624
255.7593-0.70352.94212.6785-1.49286.80870.1750.0715-0.1635-0.3841-0.054-0.28970.27260.5541-0.13020.3879-0.03510.09070.2869-0.02330.330777.003353.533758.8573
262.92740.1938-0.21446.00910.46622.46460.0245-0.2140.3919-0.0480.0522-0.0466-0.51950.2091-0.06660.3846-0.0810.05310.2725-0.03370.231573.248467.42465.2031
279.4091-3.1349-2.32451.29030.88363.62980.1288-1.20670.63661.14170.3446-0.2657-0.91680.315-0.58411.1268-0.0480.0510.8895-0.22510.392271.221777.521489.7243
281.7789-1.0806-0.21566.75071.75412.1191-0.1189-0.76190.24340.75730.322-0.4671-0.5210.0953-0.19760.6573-0.1515-0.02580.666-0.12730.356975.985468.239881.5435
292.88392.3754-0.98672.0365-1.0621.1128-0.134-0.74490.1730.57450.16250.4430.14930.25050.17131.31680.53550.53571.89970.07441.432459.7374.57579.5251
302.7779-0.5905-1.86184.97153.86675.1447-0.0516-0.0807-0.188-0.27060.0485-0.15410.14820.3249-0.03760.2930.02520.00020.2660.03010.245369.472641.31761.4636
313.3536-0.49020.49083.9251-1.0193.4927-0.0427-0.0522-0.02830.0945-0.02070.06670.10290.0910.07110.2936-0.03090.02290.26120.02830.286964.158845.288865.2345
323.5732-2.0561-2.8193.73550.27214.0156-0.3904-0.60540.8890.79170.42581.1445-0.5265-0.6395-0.08270.85070.10170.07160.54410.06490.79451.400955.296477.4342
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -3:93)A-3 - 93
2X-RAY DIFFRACTION2(chain A and resid 94:148)A94 - 148
3X-RAY DIFFRACTION3(chain A and resid 149:199)A149 - 199
4X-RAY DIFFRACTION4(chain A and resid 200:226)A200 - 226
5X-RAY DIFFRACTION5(chain A and resid 239:268)A239 - 268
6X-RAY DIFFRACTION6(chain A and resid 269:286)A269 - 286
7X-RAY DIFFRACTION7(chain A and resid 287:362)A287 - 362
8X-RAY DIFFRACTION8(chain A and resid 363:381)A363 - 381
9X-RAY DIFFRACTION9(chain B and resid -2:42)B-2 - 42
10X-RAY DIFFRACTION10(chain B and resid 43:165)B43 - 165
11X-RAY DIFFRACTION11(chain B and resid 166:214)B166 - 214
12X-RAY DIFFRACTION12(chain B and resid 215:241)B215 - 241
13X-RAY DIFFRACTION13(chain B and resid 242:309)B242 - 309
14X-RAY DIFFRACTION14(chain B and resid 310:315)B310 - 315
15X-RAY DIFFRACTION15(chain B and resid 316:368)B316 - 368
16X-RAY DIFFRACTION16(chain B and resid 369:382)B369 - 382
17X-RAY DIFFRACTION17(chain C and resid -3:1)C-3 - 1
18X-RAY DIFFRACTION18(chain C and resid 2:126)C2 - 126
19X-RAY DIFFRACTION19(chain C and resid 137:152)C137 - 152
20X-RAY DIFFRACTION20(chain C and resid 153:234)C153 - 234
21X-RAY DIFFRACTION21(chain C and resid 235:243)C235 - 243
22X-RAY DIFFRACTION22(chain C and resid 244:309)C244 - 309
23X-RAY DIFFRACTION23(chain C and resid 310:361)C310 - 361
24X-RAY DIFFRACTION24(chain C and resid 362:382)C362 - 382
25X-RAY DIFFRACTION25(chain D and resid -3:40)D-3 - 40
26X-RAY DIFFRACTION26(chain D and resid 41:126)D41 - 126
27X-RAY DIFFRACTION27(chain D and resid 137:153)D137 - 153
28X-RAY DIFFRACTION28(chain D and resid 154:227)D154 - 227
29X-RAY DIFFRACTION29(chain D and resid 228:235)D228 - 235
30X-RAY DIFFRACTION30(chain D and resid 236:278)D236 - 278
31X-RAY DIFFRACTION31(chain D and resid 279:357)D279 - 357
32X-RAY DIFFRACTION32(chain D and resid 358:382)D358 - 382

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  • 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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