[English] 日本語
Yorodumi
- PDB-3o3n: (R)-2-hydroxyisocaproyl-CoA dehydratase in complex with its subst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o3n
Title(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with its substrate (R)-2-hydroxyisocaproyl-CoA
Components
  • alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
  • beta-subunit 2-hydroxyacyl-CoA dehydratase
KeywordsLYASE / atypical dehydratase
Function / homology
Function and homology information


(R)-2-hydroxyisocaproyl-CoA dehydratase / L-leucine metabolic process / hydro-lyase activity / 4 iron, 4 sulfur cluster binding / metal ion binding
Similarity search - Function
Substrate Binding Domain Of Dnak; Chain:A; Domain 2 - #370 / Rossmann fold - #11890 / Rossmann fold - #11900 / FldB/FldC dehydratase alpha/beta subunit / 2-hydroxyglutaryl-CoA dehydratase, D-component / Substrate Binding Domain Of Dnak; Chain:A; Domain 2 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
HYDROSULFURIC ACID / Chem-IRC / IRON/SULFUR CLUSTER / (R)-2-hydroxyisocaproyl-CoA dehydratase beta subunit / (R)-2-hydroxyisocaproyl-CoA dehydratase alpha subunit
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKnauer, S.H. / Buckel, W. / Dobbek, H.
CitationJournal: J.Am.Chem.Soc. / Year: 2011
Title: Structural Basis for Reductive Radical Formation and Electron Recycling in (R)-2-Hydroxyisocaproyl-CoA Dehydratase.
Authors: Knauer, S.H. / Buckel, W. / Dobbek, H.
History
DepositionJul 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
B: beta-subunit 2-hydroxyacyl-CoA dehydratase
C: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
D: beta-subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,24812
Polymers180,0104
Non-polymers3,2388
Water21,7261206
1
A: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
B: beta-subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6246
Polymers90,0052
Non-polymers1,6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-72 kcal/mol
Surface area28460 Å2
MethodPISA
2
C: alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase
D: beta-subunit 2-hydroxyacyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6246
Polymers90,0052
Non-polymers1,6194
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-72 kcal/mol
Surface area28480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.648, 126.683, 177.699
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 2 types, 4 molecules ACBD

#1: Protein alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase


Mass: 46383.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Gene: hadB / Plasmid: pASK-IBA 3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon Plus-RIL / References: UniProt: Q5U924
#2: Protein beta-subunit 2-hydroxyacyl-CoA dehydratase


Mass: 43621.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Gene: hadC / Plasmid: pASK-IBA 3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) CodonPlus-RIL / References: UniProt: Q5U923

-
Non-polymers , 4 types, 1214 molecules

#3: Chemical
ChemComp-SF4 / IRON/SULFUR CLUSTER / Iron–sulfur cluster


Mass: 351.640 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe4S4
#4: Chemical ChemComp-IRC / S-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl ]oxy-hydroxy-phosphoryl]oxy-2-hydroxy-3,3-dimethyl-butanoyl]amino]propanoylamino]ethyl] (2R)-2-hydroxy-4-methyl-pentanethioate / (R)-2-hydroxy-4-methylpentanoyl-CoA


Mass: 881.677 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46N7O18P3S
#5: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2S
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1206 / 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: 2.21 Å3/Da / Density % sol: 44.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: reservoir solution: 23 % PEG 3350, 0.1MBis-Tris Prior to freezing in liquid nitrogen the crystal was soaked in 0.1M Bis-Tris, 20 % PEG 3350, 25 % PEG 400 and 3.8 mM (R)-2-hydroxyisocaproyl- ...Details: reservoir solution: 23 % PEG 3350, 0.1MBis-Tris Prior to freezing in liquid nitrogen the crystal was soaked in 0.1M Bis-Tris, 20 % PEG 3350, 25 % PEG 400 and 3.8 mM (R)-2-hydroxyisocaproyl-CoA for 30 minutes, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 14, 2008
Details: Double crystal monochromator with 2 sets of mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 71669 / Num. obs: 71258 / % possible obs: 99.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Rsym value: 0.099 / Net I/σ(I): 14.4
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.76 / Rsym value: 0.473 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
CNS1.2refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3O3M

3o3m


Resolution: 2.3→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 3519 5 %RANDOM
Rwork0.2278 ---
all0.2345 71669 --
obs0.2345 71258 99.4 %-
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12279 0 146 1206 13631
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d1.382
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dtt.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4fs4s.par
X-RAY DIFFRACTION52hi_CoA_fs4.par

+
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