[English] 日本語
Yorodumi
- PDB-6abw: Crystal structure of citrate synthase (Msed_0281) from Metallosph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6abw
TitleCrystal structure of citrate synthase (Msed_0281) from Metallosphaera sedula in complex with acetyl-CoA
ComponentsCitrate synthase
KeywordsTRANSFERASE / Citrate synthase / Metallosphaera sedula
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / : / tricarboxylic acid cycle / carbohydrate metabolic process / membrane / cytoplasm
Similarity search - Function
: / 2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain ...: / 2-methylcitrate synthase/citrate synthase type I / Citrate synthase, bacterial-type / Citrate Synthase; domain 1 / Citrate Synthase, domain 1 / Cytochrome p450-Terp; domain 2 / Cytochrome P450-Terp, domain 2 / Citrate synthase active site / Citrate synthase signature. / Citrate synthase-like, large alpha subdomain / Citrate synthase / Citrate synthase-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETYL COENZYME *A / Citrate synthase
Similarity search - Component
Biological speciesMetallosphaera sedula (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsLee, S.-H. / Kim, K.-J.
CitationJournal: Biochem. Biophys. Res. Commun. / Year: 2019
Title: Crystal structure and biochemical properties of msed_0281, the citrate synthase from Metallosphaera sedula.
Authors: Lee, S.H. / Kim, K.J.
History
DepositionJul 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7554
Polymers43,7611
Non-polymers9943
Water4,396244
1
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,5098
Polymers87,5222
Non-polymers1,9886
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area10680 Å2
ΔGint-38 kcal/mol
Surface area28000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.609, 94.806, 129.863
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-730-

HOH

21A-738-

HOH

-
Components

#1: Protein Citrate synthase


Mass: 43760.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Metallosphaera sedula (strain ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2) (archaea)
Strain: ATCC 51363 / DSM 5348 / JCM 9185 / NBRC 15509 / TH2 / Gene: Msed_0281 / Production host: Escherichia coli (E. coli)
References: UniProt: A4YDF6, citrate synthase (unknown stereospecificity)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACO / ACETYL COENZYME *A


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 35% v/v (+/-)-2-Methyl-2,4- pentandiol (MPD), 0.1 M Bis-Tris, pH 5.0, 0.2 M ammonium acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.72→64.94 Å / Num. obs: 39803 / % possible obs: 98.1 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 40.3
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.293 / Num. unique obs: 1928

-
Processing

Software
NameVersionClassification
HKL-2000data reduction
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GVM

1gvm


Resolution: 1.72→64.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.164 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.101
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1956 1971 5 %RANDOM
Rwork0.1499 ---
obs0.1522 37819 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 109.41 Å2 / Biso mean: 21.223 Å2 / Biso min: 6.14 Å2
Baniso -1Baniso -2Baniso -3
1--0.93 Å20 Å20 Å2
2--1.63 Å20 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.72→64.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 63 244 3227
Biso mean--41.68 32.75 -
Num. residues----369
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0193050
X-RAY DIFFRACTIONr_bond_other_d0.0020.022862
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9914135
X-RAY DIFFRACTIONr_angle_other_deg1.06436626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8995368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.61623.385130
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83115515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2991519
X-RAY DIFFRACTIONr_chiral_restr0.1990.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213331
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02637
LS refinement shellResolution: 1.723→1.768 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 153 -
Rwork0.228 2650 -
all-2803 -
obs--94.16 %

+
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