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- PDB-6sda: Bd2924 C10 acyl-coenzymeA bound form -

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Basic information

Entry
Database: PDB / ID: 6sda
TitleBd2924 C10 acyl-coenzymeA bound form
ComponentsProbable acyl-CoA dehydrogenase
KeywordsOXIDOREDUCTASE / acyl-CoA dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors / acyl-CoA dehydrogenase activity / flavin adenine dinucleotide binding
Similarity search - Function
Adaptive response protein AidB, N-terminal / Adaptive response protein AidB N-terminal domain / Acyl-CoA dehydrogenases signature 2. / Acyl-CoA dehydrogenase, conserved site / Acyl-CoA dehydrogenase/oxidase C-terminal / Acyl-CoA dehydrogenase, C-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain / Acyl-CoA dehydrogenase, middle domain / Acyl-CoA dehydrogenase/oxidase, N-terminal and middle domain superfamily / Acyl-CoA dehydrogenase-like, C-terminal
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / decanoyl-CoA / Probable acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus HD100 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsLovering, A.L. / Harding, C.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Councilstudentship United Kingdom
CitationJournal: Proteins / Year: 2019
Title: Target highlights in CASP13: Experimental target structures through the eyes of their authors.
Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / ...Authors: Lepore, R. / Kryshtafovych, A. / Alahuhta, M. / Veraszto, H.A. / Bomble, Y.J. / Bufton, J.C. / Bullock, A.N. / Caba, C. / Cao, H. / Davies, O.R. / Desfosses, A. / Dunne, M. / Fidelis, K. / Goulding, C.W. / Gurusaran, M. / Gutsche, I. / Harding, C.J. / Hartmann, M.D. / Hayes, C.S. / Joachimiak, A. / Leiman, P.G. / Loppnau, P. / Lovering, A.L. / Lunin, V.V. / Michalska, K. / Mir-Sanchis, I. / Mitra, A.K. / Moult, J. / Phillips Jr., G.N. / Pinkas, D.M. / Rice, P.A. / Tong, Y. / Topf, M. / Walton, J.D. / Schwede, T.
History
DepositionJul 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable acyl-CoA dehydrogenase
B: Probable acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8205
Polymers111,3272
Non-polymers2,4933
Water11,800655
1
A: Probable acyl-CoA dehydrogenase
B: Probable acyl-CoA dehydrogenase
hetero molecules

A: Probable acyl-CoA dehydrogenase
B: Probable acyl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,64010
Polymers222,6544
Non-polymers4,9866
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area20460 Å2
ΔGint-93 kcal/mol
Surface area66180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.266, 134.647, 133.179
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-972-

HOH

21B-973-

HOH

31B-998-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 3 - 505 / Label seq-ID: 3 - 505

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Probable acyl-CoA dehydrogenase


Mass: 55663.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus HD100 (bacteria)
Strain: ATCC 15356 / DSM 50701 / NCIB 9529 / HD100 / Gene: Bd2924 / Production host: Escherichia coli (E. coli)
References: UniProt: Q6MJ59, Oxidoreductases; Acting on the CH-CH group of donors; With unknown physiological acceptors
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 921.783 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H54N7O17P3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MIB buffer (malonate, imidazole, boric acid) pH 6 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97612 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97612 Å / Relative weight: 1
ReflectionResolution: 1.869→133.18 Å / Num. obs: 93777 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Net I/σ(I): 19.3
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.87-1.9711.50.766156658135890.8810.2340.8022.5
5.91-133.1812.20.0413884131810.9990.0120.04349.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
Aimless0.5.31data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→46.052 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.34
RfactorNum. reflection% reflection
Rfree0.191 4701 5.02 %
Rwork0.161 --
obs0.1626 93716 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 147.72 Å2 / Biso mean: 41.2408 Å2 / Biso min: 16.85 Å2
Refinement stepCycle: final / Resolution: 1.87→46.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 165 655 8620
Biso mean--68.02 45.21 -
Num. residues----1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088171
X-RAY DIFFRACTIONf_angle_d1.18211085
X-RAY DIFFRACTIONf_chiral_restr0.061236
X-RAY DIFFRACTIONf_plane_restr0.0061406
X-RAY DIFFRACTIONf_dihedral_angle_d14.5682991
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4652X-RAY DIFFRACTION6.648TORSIONAL
12B4652X-RAY DIFFRACTION6.648TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.87-1.890.30051490.24662965
1.89-1.91230.28991420.22712952
1.9123-1.93560.25671530.21132925
1.9356-1.96010.2221400.19982960
1.9601-1.98590.24051630.18522900
1.9859-2.01310.22891660.18552967
2.0131-2.04190.22721620.18992933
2.0419-2.07230.21951570.17632926
2.0723-2.10470.20151560.17582977
2.1047-2.13920.1741450.17262941
2.1392-2.17610.24131380.16142927
2.1761-2.21570.20811510.17162971
2.2157-2.25830.18051560.16372976
2.2583-2.30440.19581620.15972923
2.3044-2.35450.19871600.16152938
2.3545-2.40930.20531510.16692961
2.4093-2.46950.20911610.16062935
2.4695-2.53630.18741600.17132972
2.5363-2.61090.21041670.16732959
2.6109-2.69520.19591660.17532940
2.6952-2.79150.21171650.17412984
2.7915-2.90320.21531520.16832948
2.9032-3.03530.21621620.17422965
3.0353-3.19530.22361530.182994
3.1953-3.39550.1991660.16622969
3.3955-3.65750.18071540.16382990
3.6575-4.02540.17351630.14993011
4.0254-4.60740.15421560.12163016
4.6074-5.80310.1661840.14233016
5.8031-46.0520.15281410.14963174
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)
10.92790.37270.20390.96370.1270.5515-0.02710.2031-0.1589-0.22780.1035-0.26660.06990.1098-0.05270.2876-0.02710.06670.2789-0.04730.26814.7291-32.71944.7095
20.72670.3654-0.07981.764-0.09060.78920.0903-0.04620.19150.0278-0.07280.0774-0.08110.0134-0.01460.186-0.03680.00930.1931-0.00250.2522-1.5394-13.378617.0636
31.50280.18010.26420.67460.27851.0147-0.02350.2147-0.0668-0.26050.07420.0388-0.0281-0.007-0.04030.255-0.036-0.02120.2216-0.02180.1747-13.113-35.99632.2166
42.16750.08-0.22590.8868-0.56312.2945-0.26240.6133-0.0048-0.24540.29110.43320.0142-0.7789-0.07610.4784-0.1125-0.16390.51440.09210.3402-26.1506-29.0201-8.3366
51.2078-0.34890.61760.67060.10280.8560.1425-0.4342-0.15940.1766-0.07050.01480.1652-0.332-0.04450.2873-0.137-0.02640.43610.09480.2534-29.0562-48.118936.6087
60.78650.0644-0.35381.5219-0.18140.35510.1903-0.1874-0.5644-0.1623-0.0265-0.01830.47260.0737-0.08690.5481-0.0914-0.2310.27180.12140.5811-16.1786-67.706531.1676
71.78060.32380.49630.29180.39661.14590.0839-0.1047-0.1549-0.0113-0.02460.0620.1112-0.1471-0.0520.2033-0.0405-0.03710.21850.04320.2072-30.4828-45.037318.7542
81.78470.0513-0.1590.90550.63931.78770.11750.2461-0.2765-0.209-0.1260.0582-0.0567-0.2159-0.01190.2731-0.0279-0.08750.3026-0.00680.3282-40.5951-51.58735.2743
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 168 )B3 - 168
2X-RAY DIFFRACTION2chain 'B' and (resid 169 through 285 )B169 - 285
3X-RAY DIFFRACTION3chain 'B' and (resid 286 through 449 )B286 - 449
4X-RAY DIFFRACTION4chain 'B' and (resid 450 through 505 )B450 - 505
5X-RAY DIFFRACTION5chain 'A' and (resid 3 through 166 )A3 - 166
6X-RAY DIFFRACTION6chain 'A' and (resid 169 through 285 )A169 - 285
7X-RAY DIFFRACTION7chain 'A' and (resid 286 through 449 )A286 - 449
8X-RAY DIFFRACTION8chain 'A' and (resid 450 through 505 )A450 - 505

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