[English] 日本語
Yorodumi
- PDB-4ehu: Activator of the 2-Hydroxyisocaproyl-CoA Dehydratase from Clostri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ehu
TitleActivator of the 2-Hydroxyisocaproyl-CoA Dehydratase from Clostridium difficile with bound ADPNP
ComponentsActivator of 2-hydroxyisocaproyl-CoA dehydratase
KeywordsELECTRON TRANSPORT / actin fold / ATPase / electron transfer / ATP/ADP binding / 2-hydroxyisocaproyl-CoA dehydratase binding
Function / homology
Function and homology information


L-leucine metabolic process / Hydrolases / 4 iron, 4 sulfur cluster binding / hydrolase activity / ATP binding / metal ion binding
Similarity search - Function
CoA enzyme activase / : / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / IRON/SULFUR CLUSTER / 2-hydroxyisocaproyl-CoA dehydratase activator
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKnauer, S.H. / Dobbek, H.
CitationJournal: Biochemistry / Year: 2012
Title: On the ATP-Dependent Activation of the Radical Enzyme (R)-2-Hydroxyisocaproyl-CoA Dehydratase.
Authors: Knauer, S.H. / Buckel, W. / Dobbek, H.
History
DepositionApr 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _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_comp_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.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_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_conn.ptnr2_label_seq_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: Activator of 2-hydroxyisocaproyl-CoA dehydratase
B: Activator of 2-hydroxyisocaproyl-CoA dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,97013
Polymers59,3122
Non-polymers1,65911
Water9,188510
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-90 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.105, 158.259, 62.988
Angle α, β, γ (deg.)90.00, 111.97, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

21A-437-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Activator of 2-hydroxyisocaproyl-CoA dehydratase


Mass: 29655.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Gene: hadI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) CodonPlus-RIL / References: UniProt: Q5U925

-
Non-polymers , 6 types, 521 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 510 / 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: 2.58 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 21 mg/mL protein in 50 mM MOPS, pH 7.2, 0.2 M sodium chloride, 3 mM ADPNP, 7.5 mM magnesium chloride, 1.9 mM D-desthiobiotin, 1.5 mM DTT, 6 mM sodium dithionite, reservoir: 3.5 M ammonium ...Details: 21 mg/mL protein in 50 mM MOPS, pH 7.2, 0.2 M sodium chloride, 3 mM ADPNP, 7.5 mM magnesium chloride, 1.9 mM D-desthiobiotin, 1.5 mM DTT, 6 mM sodium dithionite, reservoir: 3.5 M ammonium acetate, 0.1 M Tris-HCl, pH 8.5 (drop: 2 uL + 2 uL), VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
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: May 27, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 76243 / Num. obs: 76243 / % possible obs: 96.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.056 / Net I/σ(I): 10.27
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.74 / Num. unique all: 13033 / Rsym value: 0.411 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.1_357)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EHT

4eht


Resolution: 1.6→25.171 Å / SU ML: 0.19 / σ(F): 1.99 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 3812 5 %RANDOM
Rwork0.1714 ---
obs0.1727 76243 96.84 %-
all-76243 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.919 Å2 / ksol: 0.394 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.2855 Å2-0 Å27.8745 Å2
2---3.8226 Å2-0 Å2
3---2.5371 Å2
Refinement stepCycle: LAST / Resolution: 1.6→25.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 87 510 4521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084141
X-RAY DIFFRACTIONf_angle_d1.5375615
X-RAY DIFFRACTIONf_dihedral_angle_d14.691552
X-RAY DIFFRACTIONf_chiral_restr0.092667
X-RAY DIFFRACTIONf_plane_restr0.004717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65720.27253920.23797443X-RAY DIFFRACTION100
1.6572-1.72350.2633900.22297407X-RAY DIFFRACTION99
1.7235-1.80190.24513880.19677366X-RAY DIFFRACTION99
1.8019-1.89690.23893850.19217300X-RAY DIFFRACTION98
1.8969-2.01570.22653830.17647291X-RAY DIFFRACTION98
2.0157-2.17130.21053800.1737213X-RAY DIFFRACTION96
2.1713-2.38960.20213740.15997101X-RAY DIFFRACTION95
2.3896-2.7350.20353710.16237051X-RAY DIFFRACTION94
2.735-3.44450.17173700.16667040X-RAY DIFFRACTION94
3.4445-25.17410.16943790.1577200X-RAY DIFFRACTION96
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)
10.8717-0.1592-0.29051.94790.68671.1788-0.0084-0.0273-0.11950.0464-0.0196-0.21910.17120.15730.03910.14710.02110.02560.10570.03370.120614.8662-17.1028-12.7253
21.57910.1165-0.13511.7835-0.28891.0204-0.0249-0.12810.20370.1355-0.1082-0.1904-0.20540.11990.12540.1798-0.0542-0.02780.14830.00570.226226.72521.8866-20.7438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

+
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