[English] 日本語
Yorodumi
- PDB-2vdj: Crystal Structure of Homoserine O-acetyltransferase (metA) from B... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vdj
TitleCrystal Structure of Homoserine O-acetyltransferase (metA) from Bacillus Cereus with Homoserine
ComponentsHOMOSERINE O-SUCCINYLTRANSFERASE
KeywordsTRANSFERASE / METHIONINE BIOSYNTHESIS / AMINO-ACID BIOSYNTHESIS / HOMOSERINE TRANSACETYLASE / HOMOSERINE TRANSSUCCINYLASE / HOMOSERINE / ACYLTRANSFERASE
Function / homology
Function and homology information


homoserine O-succinyltransferase activity / L-methionine biosynthetic process from homoserine via O-succinyl-L-homoserine and cystathionine / homoserine O-acetyltransferase / homoserine O-acetyltransferase activity / cytoplasm
Similarity search - Function
Homoserine O-succinyltransferase MetA / MetA family / Homoserine O-succinyltransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-HOMOSERINE / Homoserine O-acetyltransferase
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsZubieta, C. / Arkus, K.A.J. / Cahoon, R.E. / Jez, J.M.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: A Single Amino Acid Change is Responsible for Evolution of Acyltransferase Specificity in Bacterial Methionine Biosynthesis.
Authors: Zubieta, C. / Arkus, K.A.J. / Cahoon, R.E. / Jez, J.M.
History
DepositionOct 10, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.3Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HOMOSERINE O-SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6073
Polymers35,3921
Non-polymers2152
Water2,936163
1
A: HOMOSERINE O-SUCCINYLTRANSFERASE
hetero molecules

A: HOMOSERINE O-SUCCINYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2156
Polymers70,7842
Non-polymers4304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/41
Buried area4660 Å2
ΔGint-24.9 kcal/mol
Surface area29390 Å2
MethodPQS
Unit cell
Length a, b, c (Å)96.390, 96.390, 75.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

-
Components

#1: Protein HOMOSERINE O-SUCCINYLTRANSFERASE / HOMOSERINE O-TRANSSUCCINYLASE / HTSHOMOSERINE O-ACETYLTRANSFERASE


Mass: 35392.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: PROTEIN IS A PHYSIOLOGICAL DIMER, DIMER FORMED BY CRYSTALLOGRAPHIC TWO-FOLD
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BL-21 CODON PLUS
References: UniProt: Q72X44, homoserine O-succinyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-HSE / L-HOMOSERINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSULFATE ION (SO4): SULFATE FROM CRYSTALLIZATION CONDITIONS L-HOMOSERINE (HSE): CO-CRYSTALLIZED WITH ...SULFATE ION (SO4): SULFATE FROM CRYSTALLIZATION CONDITIONS L-HOMOSERINE (HSE): CO-CRYSTALLIZED WITH HOMOSERINE 10MM
Sequence detailsRESIDUES 1-16 AND 298-301 WERE NOT VISIBLE IN XTAL STRUCTURE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 8
Details: 1.6M AMMONIUM SULFATE, 0.1 M TRIS, PH 8, 10MM HOMOSERINE

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→100 Å / Num. obs: 22903 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.85
Reflection shellResolution: 2→2.12 Å / Redundancy: 7 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.59 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GHR

2ghr


Resolution: 2→19.47 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 8.837 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1144 5 %RANDOM
Rwork0.199 ---
obs0.201 21729 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.18 Å2
Refinement stepCycle: LAST / Resolution: 2→19.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 13 163 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212278
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9871.9463075
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7245266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.73924.355124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.22515406
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7971514
X-RAY DIFFRACTIONr_chiral_restr0.0690.2329
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021739
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1730.2948
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.21526
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2169
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1540.255
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.01731378
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66952143
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5371026
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6979932
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.314 86
Rwork0.275 1645
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)
19.4595-18.9459-4.884339.88782.667228.58770.0331.1846-1.41640.5619-1.09372.16250.5538-1.31241.06070.0644-0.2170.01570.0783-0.14670.1264-26.115-47.924-19.648
24.20041.196-0.32732.877-1.2146.4764-0.08040.11690.1038-0.15090.06150.2260.1512-0.73780.0189-0.1342-0.0524-0.0310.2127-0.0303-0.0459-40.455-22.2656.432
30.60570.1760.08811.33530.20471.53030.0108-0.0174-0.0669-0.0462-0.026-0.0647-0.0338-0.00890.01520.03360.00450.00610.0692-0.0378-0.0325-23.698-14.4116.982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 29
2X-RAY DIFFRACTION2A30 - 102
3X-RAY DIFFRACTION3A103 - 297

+
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