[English] 日本語
Yorodumi
- PDB-8xu2: DaCS-citrate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xu2
TitleDaCS-citrate complex
Componentscitrate synthase
KeywordsTRANSFERASE / citrate synthase / citrate cleavage / reversible
Function / homology
Function and homology information


citrate synthase (unknown stereospecificity) / citrate synthase activity / tricarboxylic acid cycle / carbohydrate metabolic process
Similarity search - Function
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
Similarity search - Domain/homology
CITRIC ACID / citrate synthase (unknown stereospecificity)
Similarity search - Component
Biological speciesDesulfurella acetivorans A63 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsYang, L.Y. / Fang, Y.J.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: DaCS-citrate complex
Authors: Yang, L.Y. / Fang, Y.J.
History
DepositionJan 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: citrate synthase
B: citrate synthase
C: citrate synthase
D: citrate synthase
E: citrate synthase
F: citrate synthase
G: citrate synthase
H: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,12616
Polymers393,5898
Non-polymers1,5378
Water27,4011521
1
A: citrate synthase
B: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-64 kcal/mol
Surface area29750 Å2
MethodPISA
2
C: citrate synthase
D: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10340 Å2
ΔGint-63 kcal/mol
Surface area29570 Å2
MethodPISA
3
E: citrate synthase
F: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-63 kcal/mol
Surface area29620 Å2
MethodPISA
4
G: citrate synthase
H: citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7814
Polymers98,3972
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10300 Å2
ΔGint-63 kcal/mol
Surface area29600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)362.335, 362.335, 77.886
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein
citrate synthase


Mass: 49198.590 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfurella acetivorans A63 (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A7C6A739, citrate synthase (unknown stereospecificity)
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1521 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.91 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium chloride, 0.1 M HEPES pH 7.5 and 35% v/v Pentaerythritol propoxylate (5/4 PO/OH)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.18→24.66 Å / Num. obs: 191541 / % possible obs: 97.5 % / Redundancy: 8.2 % / CC1/2: 0.991 / Net I/σ(I): 32
Reflection shellResolution: 2.19→2.22 Å / Redundancy: 8 % / Rmerge(I) obs: 0.567 / Num. unique obs: 9494 / CC star: 0.964 / Rpim(I) all: 0.21 / Rrim(I) all: 0.606

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.19→24.66 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.398 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20347 9668 5.1 %RANDOM
Rwork0.17488 ---
obs0.17633 181722 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.24 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.19→24.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27443 0 104 1522 29069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01228299
X-RAY DIFFRACTIONr_bond_other_d0.0010.01626163
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.64338377
X-RAY DIFFRACTIONr_angle_other_deg0.4341.55660995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42553491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.98510144
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.741104828
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0630.24155
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0231853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025547
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_it3.2583.85913940
X-RAY DIFFRACTIONr_mcbond_other3.2583.85913940
X-RAY DIFFRACTIONr_mcangle_it4.7475.77417415
X-RAY DIFFRACTIONr_mcangle_other4.7475.77517416
X-RAY DIFFRACTIONr_scbond_it3.5054.12314359
X-RAY DIFFRACTIONr_scbond_other3.5044.12414356
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2796.0720955
X-RAY DIFFRACTIONr_long_range_B_refined7.13248.20933881
X-RAY DIFFRACTIONr_long_range_B_other7.12448.00733607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.246 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 731 -
Rwork0.236 13244 -
obs--96.64 %

+
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