[English] 日本語
Yorodumi
- PDB-4zbg: Crystal Structure of a GNAT family Acetyltransferase from Brucell... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zbg
TitleCrystal Structure of a GNAT family Acetyltransferase from Brucella melitensis in complex with Acetyl-CoA
ComponentsAcetyltransferase
KeywordsTRANSFERASE / SGCID / N-acetyltransferase / Acyl_CoA_acyltransferase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETYL COENZYME *A / Acetyltransferase
Similarity search - Component
Biological speciesBrucella abortus str. 2308 A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a GNAT family Acetyltransferase from Brucella melitensis in complex with Acetyl-CoA
Authors: SSGCID / Dranow, D.M. / Trakaki, T. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 14, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list ...entity_src_gen / pdbx_struct_oper_list / pdbx_validate_close_contact / reflns_shell
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2Sep 27, 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: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5333
Polymers18,6311
Non-polymers9022
Water4,342241
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.810, 57.110, 44.060
Angle α, β, γ (deg.)90.000, 96.530, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Acetyltransferase /


Mass: 18631.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus str. 2308 A (bacteria)
Strain: 2308 A / Gene: BAAA_2000484 / Plasmid: BrabA.17468.b.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: C4IR59
#2: Chemical ChemComp-ACO / ACETYL COENZYME *A / Acetyl-CoA


Mass: 809.571 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H38N7O17P3S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 241 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: BrabA.17468.b.B1.PS02320 at 10.4mg/ml, mixed with 4mM acetyl-CoA, then 1:1 with MCSG1(c12): 0.1M Bis-Tris:HCl, pH=6.5, 25% PEG-3350, cryo-protected with 20% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionNumber: 218334 / Rmerge(I) obs: 0.04 / Χ2: 0.99 / D res high: 1.25 Å / Num. obs: 40267 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
3.955.5985810.025
3.233.95108810.025
2.83.23128010.028
2.52.8144610.031
2.282.5161010.032
2.112.28173310.033
1.982.11189810.037
1.861.98195710.039
1.771.86211310.048
1.691.77221010.055
1.611.69231310.066
1.551.61240010.078
1.491.55248210.091
1.441.49259110.111
1.41.44267210.137
1.361.4274310.169
1.321.36287310.203
1.281.32286410.238
1.251.28268210.26
ReflectionResolution: 1.25→50 Å / Num. obs: 40267 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 9.23 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.04 / Rrim(I) all: 0.045 / Χ2: 0.991 / Net I/σ(I): 23.66 / Num. measured all: 218334
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.25-1.2840.9320.264.8210635295426820.390.8
1.28-1.320.9580.2386.3214220290928640.26798.5
1.32-1.360.970.2037.8115682287628730.22599.9
1.36-1.40.9810.1699.4115101274027430.188100
1.4-1.440.9860.13711.3514701267326720.152100
1.44-1.490.9910.11113.7514326259225910.122100
1.49-1.550.9940.09116.5213803248224820.1100
1.55-1.610.9960.07819.1513368240224000.08699.9
1.61-1.690.9960.06622.1912935231423130.073100
1.69-1.770.9970.05525.7912392220922100.061100
1.77-1.860.9980.04828.9111882211621130.05299.9
1.86-1.980.9990.03935.3711071195319570.043100
1.98-2.110.9990.03738.8210718189818980.04100
2.11-2.280.9990.03342.539814173317330.037100
2.28-2.50.9990.03244.839071161416100.03599.8
2.5-2.80.9990.03147.598204144514460.034100
2.8-3.230.9990.02850.867234128312800.03199.8
3.23-3.950.9990.02553.836136108910880.02899.9
3.95-5.590.9990.02554.4647398598580.02899.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RS2

4rs2


Resolution: 1.25→26.291 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.163 2003 4.98 %
Rwork0.1417 38238 -
obs0.1429 40241 99.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.45 Å2 / Biso mean: 15.191 Å2 / Biso min: 4.7 Å2
Refinement stepCycle: final / Resolution: 1.25→26.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 57 247 1466
Biso mean--16.16 26.29 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061324
X-RAY DIFFRACTIONf_angle_d1.2041803
X-RAY DIFFRACTIONf_chiral_restr0.068183
X-RAY DIFFRACTIONf_plane_restr0.005236
X-RAY DIFFRACTIONf_dihedral_angle_d17.096498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.25-1.28120.22411280.1592451257991
1.2812-1.31590.17261480.14362699284798
1.3159-1.35460.17231300.136827772907100
1.3546-1.39830.19221250.130227592884100
1.3983-1.44830.17951450.12827062851100
1.4483-1.50630.15281460.121727742920100
1.5063-1.57480.15231420.123527642906100
1.5748-1.65780.161310.127827522883100
1.6578-1.76170.15791430.130527632906100
1.7617-1.89770.16821380.138727602898100
1.8977-2.08860.17421670.133427162883100
2.0886-2.39060.15961390.14727752914100
2.3906-3.01120.16031460.157327772923100
3.0112-26.29720.15351750.14982765294099

+
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