[English] 日本語
Yorodumi
- PDB-4tv6: Crystal Structure of Citrate Synthase Variant SbnG E151Q -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4tv6
TitleCrystal Structure of Citrate Synthase Variant SbnG E151Q
Components2-dehydro-3-deoxyglucarate aldolase
KeywordsLYASE / siderophore biosynthesis / iron / citrate synthase
Function / homology
Function and homology information


aldehyde-lyase activity / catalytic activity / metal ion binding / cytoplasm
Similarity search - Function
: / HpcH/HpaI aldolase/citrate lyase domain / HpcH/HpaI aldolase/citrate lyase / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
OXALOACETATE ION / 2-dehydro-3-deoxyglucarate aldolase / 2-dehydro-3-deoxyglucarate aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsKobylarz, M.J. / Grigg, J.C. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: SbnG, a Citrate Synthase in Staphylococcus aureus: A NEW FOLD ON AN OLD ENZYME.
Authors: Kobylarz, M.J. / Grigg, J.C. / Sheldon, J.R. / Heinrichs, D.E. / Murphy, M.E.
History
DepositionJun 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 1.2Dec 17, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2-dehydro-3-deoxyglucarate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8852
Polymers28,7541
Non-polymers1311
Water77543
1
A: 2-dehydro-3-deoxyglucarate aldolase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)173,31012
Polymers172,5236
Non-polymers7866
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 operation4_555-y,-x,-z1
crystal symmetry operation5_555-x+y,y,-z1
crystal symmetry operation6_555x,x-y,-z1
Buried area22550 Å2
ΔGint-66 kcal/mol
Surface area51150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.240, 77.240, 75.810
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number149
Space group name H-MP312
Components on special symmetry positions
IDModelComponents
11A-404-

HOH

DetailsThe biological assembly is a hexamer generated from the monomer in the asymmetric unit by the operation:-x+y,y,-z, -x+y,-x,z, x,x-y,-z, -y,x-y,z and -y,-x,-z

-
Components

#1: Protein 2-dehydro-3-deoxyglucarate aldolase


Mass: 28753.910 Da / Num. of mol.: 1 / Mutation: E151Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: Newman / Gene: sbnG, NWMN_0066 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A6QDA6, UniProt: A0A0H3K9Z0*PLUS
#2: Chemical ChemComp-OAA / OXALOACETATE ION


Mass: 131.064 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 5% (v/v) tascimate, 0.1 M HEPES, 10% PEG MME 5000, 40 mM gaunidine hydrochloride, 5 mM oxaloacetate, 5 mM coeznyme A

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→27.05 Å / Num. all: 7119 / Num. obs: 7119 / % possible obs: 87.5 % / Redundancy: 4.9 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.037 / Rrim(I) all: 0.097 / Rsym value: 0.089 / Net I/σ(I): 11.5 / Num. measured all: 34715
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym value% possible all
2.6-2.744.80.2465.1490610180.0170.0487.3
8.22-27.054.90.0420.111182270.0230.05679.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 44.21 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å18.24 Å
Translation2.5 Å18.24 Å

-
Processing

Software
NameVersionClassification
PHENIXrefinement
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→27.052 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 322 4.53 %RANDOM
Rwork0.232 6793 --
obs0.2342 7115 87.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.41 Å2 / Biso mean: 56.587 Å2 / Biso min: 15.34 Å2
Refinement stepCycle: final / Resolution: 2.6→27.052 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1753 0 9 43 1805
Biso mean--65.98 36.78 -
Num. residues----225
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031791
X-RAY DIFFRACTIONf_angle_d0.7482426
X-RAY DIFFRACTIONf_chiral_restr0.022282
X-RAY DIFFRACTIONf_plane_restr0.004315
X-RAY DIFFRACTIONf_dihedral_angle_d15.124654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6003-3.27520.31691670.26863369353688
3.2752-27.05350.26681550.21733424357987
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)
10.7665-0.7311-0.63974.6965-1.00495.5444-0.24390.30130.06570.17440.22560.76270.3414-0.77050.03330.31730.0152-0.0040.30650.08530.5262-15.0964-22.00211.4927
22.2931-0.2267-1.9275.75660.31284.5606-0.0218-0.1984-0.10960.19810.15380.13590.08360.2202-0.10190.19760.0191-0.00030.22040.04790.2711-8.891-12.32428.3895
36.5079-0.951-1.70576.30780.31285.1513-0.0552-1.62630.55971.60680.53640.2782-0.1650.0441-0.40740.65830.10320.10140.6024-0.03180.4325-10.6157-11.55326.1636
42.0830.0185-0.52196.7731-0.07261.77270.08230.26320.43040.6942-0.15612.2179-0.1605-1.38550.16870.76810.24520.16221.03370.11570.8329-20.7996-2.908822.7621
51.3734-0.4194-0.04414.6247-3.175.2148-0.6831-0.4117-0.26371.19140.5789-0.2981-0.20161.27780.08990.74630.1975-0.06660.80390.02060.2914-5.9932-20.128828.1666
62.04010.7453-0.8142.3828-1.56074.2273-0.1849-0.77880.13280.97430.45510.8971-0.24080.0463-0.56910.79420.33680.4310.8750.42470.2053-13.5833-20.03329.1581
77.2317-5.87220.80827.61080.02362.16461.3350.5377-0.1051-0.8317-0.1571-0.81831.98040.3873-1.23980.83930.3146-0.16880.9043-0.14910.57565.5718-29.174624.2809
82.07230.53970.50344.64710.88337.6457-0.3582-0.7172-0.47781.19490.77910.50261.5040.52-0.36440.83570.0970.11220.57170.19390.4619-9.832-31.092222.6368
92.09290.9891.38953.1991-1.82823.24950.07880.116-0.7382-0.0479-0.3507-0.17150.31550.40830.24050.37640.11830.05570.2196-0.02410.54557.2425-31.0615-1.1544
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 26 )A6 - 26
2X-RAY DIFFRACTION2chain 'A' and (resid 27 through 87 )A27 - 87
3X-RAY DIFFRACTION3chain 'A' and (resid 88 through 109 )A88 - 109
4X-RAY DIFFRACTION4chain 'A' and (resid 110 through 144 )A110 - 144
5X-RAY DIFFRACTION5chain 'A' and (resid 145 through 158 )A145 - 158
6X-RAY DIFFRACTION6chain 'A' and (resid 159 through 174 )A159 - 174
7X-RAY DIFFRACTION7chain 'A' and (resid 175 through 190 )A175 - 190
8X-RAY DIFFRACTION8chain 'A' and (resid 191 through 236 )A191 - 236
9X-RAY DIFFRACTION9chain 'A' and (resid 237 through 257 )A237 - 257

+
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