[English] 日本語
Yorodumi
- PDB-3mpj: Structure of the glutaryl-coenzyme A dehydrogenase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mpj
TitleStructure of the glutaryl-coenzyme A dehydrogenase
Components
  • Glutaryl-CoA dehydrogenase
  • OctapeptidePeptide
KeywordsOXIDOREDUCTASE / alpha-beta fold
Function / homology
Function and homology information


glutaryl-CoA dehydrogenase (acceptor) / acyl-CoA dehydrogenase activity / : / flavin adenine dinucleotide binding
Similarity search - Function
Acyl-CoA dehydrogenases signature 1. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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 dehydrogenases signature 1. / Acyl-CoA dehydrogenase, conserved site / Butyryl-Coa Dehydrogenase, subunit A; domain 1 / Acyl-CoA dehydrogenase/oxidase, N-terminal domain / Acyl-CoA oxidase/dehydrogenase, middle domain superfamily / 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
FLAVIN-ADENINE DINUCLEOTIDE / Glutaryl-CoA dehydrogenase
Similarity search - Component
Biological speciesDesulfococcus multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWischgoll, S. / Warkentin, E. / Boll, M. / Ermler, U.
CitationJournal: Biochemistry / Year: 2010
Title: Structural basis for promoting and preventing decarboxylation in glutaryl-coenzyme a dehydrogenases.
Authors: Wischgoll, S. / Demmer, U. / Warkentin, E. / Gunther, R. / Boll, M. / Ermler, U.
History
DepositionApr 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 5, 2012Group: Derived calculations
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
D: Glutaryl-CoA dehydrogenase
E: Glutaryl-CoA dehydrogenase
F: Glutaryl-CoA dehydrogenase
G: Glutaryl-CoA dehydrogenase
Y: Octapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,61319
Polymers261,6877
Non-polymers4,92612
Water13,998777
1
A: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
Y: Octapeptide
hetero molecules

A: Glutaryl-CoA dehydrogenase
B: Glutaryl-CoA dehydrogenase
Y: Octapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,12014
Polymers175,8366
Non-polymers3,2848
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area23090 Å2
ΔGint-194 kcal/mol
Surface area49100 Å2
MethodPISA
2
D: Glutaryl-CoA dehydrogenase
E: Glutaryl-CoA dehydrogenase
F: Glutaryl-CoA dehydrogenase
G: Glutaryl-CoA dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,05312
Polymers173,7694
Non-polymers3,2848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23170 Å2
ΔGint-194 kcal/mol
Surface area49200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.400, 250.600, 62.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31D
41E
51F
61G

-
Components

#1: Protein
Glutaryl-CoA dehydrogenase /


Mass: 43442.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfococcus multivorans (bacteria) / Gene: acd, gi228015642 / Production host: Escherichia coli (E. coli) / References: UniProt: C3UVB0, glutaryl-CoA dehydrogenase
#2: Protein/peptide Octapeptide / Peptide


Mass: 1033.128 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CLEAVED PRODUCT / Source: (gene. exp.) Desulfococcus multivorans (bacteria) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 777 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1 mM FAD, 50% (v,v) MPD, 0.1 M Tris/HCl, pH 8.5 and 0.2 M NH4H2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: mar225 / Detector: CCD / Date: Nov 15, 2006
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 133695 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 98

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SIQ

1siq


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.712 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.224 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22466 7062 5 %RANDOM
Rwork0.18094 ---
obs0.18317 133695 99.75 %-
all-133695 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.967 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.95 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17986 0 324 777 19087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02218785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6411.98125426
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80452361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.02524.418833
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.867153131
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.32615105
X-RAY DIFFRACTIONr_chiral_restr0.1250.22699
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02114305
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8861.511628
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.468218451
X-RAY DIFFRACTIONr_scbond_it2.93237086
X-RAY DIFFRACTIONr_scangle_it4.2944.56889
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B1536MEDIUM POSITIONAL0.120.5
2A1536MEDIUM POSITIONAL0.120.5
3D1536MEDIUM POSITIONAL0.150.5
4E1536MEDIUM POSITIONAL0.160.5
5F1536MEDIUM POSITIONAL0.120.5
6G1536MEDIUM POSITIONAL0.130.5
1B1445LOOSE POSITIONAL0.35
2A1445LOOSE POSITIONAL0.275
3D1445LOOSE POSITIONAL0.335
4E1445LOOSE POSITIONAL0.395
5F1445LOOSE POSITIONAL0.35
6G1445LOOSE POSITIONAL0.375
1B1536MEDIUM THERMAL1.882
2A1536MEDIUM THERMAL1.842
3D1536MEDIUM THERMAL1.932
4E1536MEDIUM THERMAL2.172
5F1536MEDIUM THERMAL1.692
6G1536MEDIUM THERMAL1.972
1B1445LOOSE THERMAL2.5910
2A1445LOOSE THERMAL2.7810
3D1445LOOSE THERMAL2.7310
4E1445LOOSE THERMAL3.1710
5F1445LOOSE THERMAL2.5210
6G1445LOOSE THERMAL2.7610
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 462 -
Rwork0.249 9552 -
obs--97.95 %
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)
10.91890.2225-0.25170.8238-0.35531.3272-0.0207-0.1331-0.16770.02870.02260.1250.148-0.2034-0.00190.0452-0.02750.02550.14590.02220.074456.899108.46140.958
20.9772-0.2277-0.32550.95890.26911.5509-0.01940.0319-0.2243-0.092-0.0002-0.18420.21330.20480.01960.07240.0550.04340.09590.0060.12294.434107.30923.269
30.9154-0.1910.2171.7696-0.94761.6237-0.2630.13480.39330.4868-0.1601-0.3715-0.65630.32880.42320.4643-0.1594-0.34370.1320.170.34775.78468.5593.174
40.8144-0.20170.16171.7536-1.14322.4655-0.1945-0.21770.04470.71840.42850.5431-0.7708-0.6827-0.23410.46050.28950.13170.30520.09360.274744.652.24420.592
50.6146-0.16720.44481.1808-0.02651.83710.09060.001-0.1887-0.0759-0.00060.210.333-0.0026-0.090.15880.0154-0.05190.07090.04670.165862.45619.1683.269
61.2963-0.37021.01010.637-0.46611.8357-0.15210.11870.17150.2149-0.1455-0.3195-0.19630.46840.29770.1785-0.0425-0.15940.29130.17480.240993.09835.72821.283
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 389
2X-RAY DIFFRACTION1A400 - 401
3X-RAY DIFFRACTION2B1 - 393
4X-RAY DIFFRACTION2B400 - 401
5X-RAY DIFFRACTION3D1 - 390
6X-RAY DIFFRACTION3D400 - 401
7X-RAY DIFFRACTION4E1 - 391
8X-RAY DIFFRACTION4E400 - 401
9X-RAY DIFFRACTION5F1 - 390
10X-RAY DIFFRACTION5F400 - 401
11X-RAY DIFFRACTION6G1 - 389
12X-RAY DIFFRACTION6G400 - 401

+
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