[English] 日本語
Yorodumi
- PDB-6sd8: Bd2924 apo-form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sd8
TitleBd2924 apo-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 / Probable acyl-CoA dehydrogenase
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.51 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 1.1Nov 6, 2019Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3May 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)112,8984
Polymers111,3272
Non-polymers1,5712
Water14,052780
1
X: Probable acyl-CoA dehydrogenase
A: Probable acyl-CoA dehydrogenase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)225,7968
Polymers222,6544
Non-polymers3,1424
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area20790 Å2
ΔGint-95 kcal/mol
Surface area67160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.750, 113.012, 89.044
Angle α, β, γ (deg.)90.000, 120.840, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-1004-

HOH

21A-1072-

HOH

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

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 AAB
2chain XXA

-
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 (strain ATCC 15356 / DSM 50701 / NCIB 9529 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 780 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 40% pentaerythritol propoxylate 15% ethanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.51→81.71 Å / Num. obs: 177144 / % possible obs: 97 % / Redundancy: 6.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.021 / Rrim(I) all: 0.055 / Net I/σ(I): 11.9 / Num. measured all: 1198412 / Scaling rejects: 221
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.51-1.556.41.26281267127890.8210.5411.3761.294.9
6.75-81.716.70.0421417121120.9950.0180.04638.799.8

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
PHENIX1.9_1692refinement
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.51→76.454 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1929 8578 4.95 %
Rwork0.1739 164817 -
obs0.1749 173395 94.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.29 Å2 / Biso mean: 37.4094 Å2 / Biso min: 15.5 Å2
Refinement stepCycle: final / Resolution: 1.51→76.454 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7802 0 106 780 8688
Biso mean--35.52 44.12 -
Num. residues----1006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078107
X-RAY DIFFRACTIONf_angle_d1.14110995
X-RAY DIFFRACTIONf_chiral_restr0.0491232
X-RAY DIFFRACTIONf_plane_restr0.0061404
X-RAY DIFFRACTIONf_dihedral_angle_d13.3092975
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4640X-RAY DIFFRACTION4.967TORSIONAL
12X4640X-RAY DIFFRACTION4.967TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.51-1.5270.38342610.3804495687
1.527-1.54490.40342670.3632511089
1.5449-1.56380.35092540.3477526990
1.5638-1.58360.3662730.3393518490
1.5836-1.60440.34462900.324519591
1.6044-1.62640.33842690.3106525591
1.6264-1.64960.32182620.2945537192
1.6496-1.67430.32152680.284532092
1.6743-1.70040.29593000.2673534993
1.7004-1.72830.29242960.2545538393
1.7283-1.75810.25642660.2466544994
1.7581-1.79010.2923010.2279543894
1.7901-1.82450.24752700.2222547194
1.8245-1.86180.21322620.2131551395
1.8618-1.90220.24172980.206547796
1.9022-1.94650.22392980.2014556196
1.9465-1.99520.21392930.2003558296
1.9952-2.04910.22512690.1846557796
2.0491-2.10940.19862830.1794563297
2.1094-2.17750.1932750.1695567997
2.1775-2.25540.18842970.1645559197
2.2554-2.34570.19173040.1569562397
2.3457-2.45240.18173040.1629562098
2.4524-2.58170.20122850.1633566398
2.5817-2.74350.18173030.1654571098
2.7435-2.95530.18593100.1637572399
2.9553-3.25270.20383050.1716571899
3.2527-3.72340.18423000.1588580899
3.7234-4.6910.14283290.1339574899
4.691-76.450.152860.1471584299
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)
10.7487-0.15730.2930.48250.0940.71940.0554-0.35810.01480.2357-0.1305-0.00860.0567-0.376-0.03750.23-0.10050.06030.4075-0.04210.2069-28.483978.0296116.6073
20.26220.01080.05490.405-0.05120.0560.162-0.0864-0.2563-0.064-0.1587-0.09370.306-0.10940.01130.435-0.1166-0.06960.19690.02990.3458-15.67558.4567111.7929
30.66210.02490.39760.18590.14770.72350.0712-0.07660.0204-0.0719-0.12080.10980.0297-0.2361-0.00160.1928-0.0206-0.0040.2791-0.05850.2306-29.293481.089498.5181
40.12360.03890.08540.06380.01580.07660.0549-0.03870.064-0.2155-0.05820.1048-0.065-0.0921-00.23560.0011-0.05460.2851-0.08140.2895-38.786774.388184.7444
50.59420.31570.27640.45920.03740.6096-0.02120.1157-0.079-0.0015-0.0116-0.17380.06580.1379-0.00020.20.02740.04170.21490.00520.21186.915692.690986.4749
60.17490.25320.05840.40580.18050.54350.0241-0.05260.13150.0258-0.13490.1215-0.1949-0.0446-00.26470.0125-0.02430.16240.0010.25910.2684112.585898.472
70.67570.36080.06290.24080.10480.3886-0.0550.17930.0385-0.12690.0340.0910.0268-0.0539-0.00110.22340.0107-0.01390.2108-0.00780.204-10.802990.199882.8604
80.4202-0.1339-0.34550.21650.00470.5759-0.24470.4767-0.091-0.24010.04960.39650.0882-0.4286-0.07840.3275-0.0137-0.15160.49790.05050.3489-22.985796.972271.5522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'X' and (resid 3 through 168 )X3 - 168
2X-RAY DIFFRACTION2chain 'X' and (resid 169 through 285 )X169 - 285
3X-RAY DIFFRACTION3chain 'X' and (resid 286 through 449 )X286 - 449
4X-RAY DIFFRACTION4chain 'X' and (resid 450 through 505 )X450 - 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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

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

-
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

Read more