[English] 日本語
Yorodumi
- PDB-4e6y: Type II citrate synthase from Vibrio vulnificus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e6y
TitleType II citrate synthase from Vibrio vulnificus.
ComponentsCitrate synthase
KeywordsTRANSFERASE / structural genomics / type II citrate synthase / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


citrate (Si)-synthase activity / membrane => GO:0016020 / tricarboxylic acid cycle / membrane / cytoplasm
Similarity search - Function
Rubrerythrin, domain 2 - #60 / 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 ...Rubrerythrin, domain 2 - #60 / 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-like, small alpha subdomain / Citrate synthase superfamily / Citrate synthase, C-terminal domain / Citrate synthase / Rubrerythrin, domain 2 / Single Sheet / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FORMIC ACID / Citrate synthase / Citrate synthase
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsOsipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Type II citrate synthase from Vibrio vulnificus.
Authors: Osipiuk, J. / Gu, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionMar 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5935
Polymers49,4091
Non-polymers1844
Water90150
1
A: Citrate synthase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)297,55630
Polymers296,4516
Non-polymers1,10524
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation9_555-x,-x+y,-z1
Buried area45080 Å2
ΔGint-270 kcal/mol
Surface area95900 Å2
2
A: Citrate synthase
hetero molecules

A: Citrate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,18510
Polymers98,8172
Non-polymers3688
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area13170 Å2
ΔGint-80 kcal/mol
Surface area33820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.717, 109.717, 153.649
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-606-

HOH

Detailsbased on PISA

-
Components

#1: Protein Citrate synthase


Mass: 49408.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: gltA, VV1_0162 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8DFP4, UniProt: A0A3Q0L1H4*PLUS, citrate (Si)-synthase
#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M sodium formate, 20 % PEG-3350, 20 mM HEPES buffer, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 22, 2012
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.5→45.4 Å / Num. all: 19591 / Num. obs: 19591 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.4 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.146 / Χ2: 2.182 / Net I/σ(I): 9.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.5417.40.9394.79581.058100
2.54-2.5917.30.8119461.148100
2.59-2.6417.40.6869521.181100
2.64-2.6917.50.6059711.266100
2.69-2.7517.30.5359481.3100
2.75-2.8217.60.469651.388100
2.82-2.8917.50.4529551.433100
2.89-2.9617.60.3399631.682100
2.96-3.0517.70.3159571.782100
3.05-3.1517.70.2499651.912100
3.15-3.2617.70.2199712.066100
3.26-3.3917.70.1879692.293100
3.39-3.5517.60.1649682.469100
3.55-3.7317.60.1459752.578100
3.73-3.9717.40.139812.589100
3.97-4.2717.40.1169962.72100
4.27-4.717.40.1079962.797100
4.7-5.3817.30.10610033.018100
5.38-6.7816.90.10810344.028100
6.78-5015.80.08311184.62698.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-2000data scaling
MOLREPphasing
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3l96

3l96
PDB Unreleased entry


Resolution: 2.5→45.4 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 17.645 / SU ML: 0.182 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.407 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2314 996 5.1 %RANDOM
Rwork0.1886 ---
all0.1907 19512 --
obs0.1907 19512 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.08 Å2 / Biso mean: 52.4796 Å2 / Biso min: 25.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0.41 Å20 Å2
2---0.83 Å20 Å2
3---1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3371 0 12 50 3433
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.023465
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.9544692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1585425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8923.476164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.12315568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4891523
X-RAY DIFFRACTIONr_chiral_restr0.1070.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212667
LS refinement shellResolution: 2.499→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 60 -
Rwork0.253 1179 -
all-1239 -
obs-1239 99.6 %
Refinement TLS params.Method: refined / Origin x: 20.9121 Å / Origin y: 25.7548 Å / Origin z: 13.5515 Å
111213212223313233
T0.0223 Å2-0.0122 Å20.0002 Å2-0.0449 Å2-0.0019 Å2--0.0412 Å2
L0.4289 °20.1203 °20.1409 °2-0.7141 °2-0.2855 °2--0.9798 °2
S-0.0145 Å °0.0256 Å °0.0013 Å °-0.0245 Å °-0.0259 Å °-0.1559 Å °-0.061 Å °0.2024 Å °0.0404 Å °

+
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