[English] 日本語
Yorodumi
- PDB-5vdb: Crystal structure of a GNAT superfamily acetyltransferase PA4794 ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5vdb
TitleCrystal structure of a GNAT superfamily acetyltransferase PA4794 in complex with bisubstrate analog 3
Componentsacetyltransferase PA4794
Keywordstransferase/transferase inhibitor / GNAT / acetyltransferase / bisubstrate inhibitor / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TRANSFERASE / transferase-transferase inhibitor complex
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / metal ion binding
Similarity search - Function
: / Acetyltransferase (GNAT) family / 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
Chem-93M / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMajorek, K.A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54 GM094585 United States
Citation
Journal: FEBS Lett. / Year: 2017
Title: Generating enzyme and radical-mediated bisubstrates as tools for investigating Gcn5-related N-acetyltransferases.
Authors: Reidl, C. / Majorek, K.A. / Dang, J. / Tran, D. / Jew, K. / Law, M. / Payne, Y. / Minor, W. / Becker, D.P. / Kuhn, M.L.
#1: Journal: J. Biol. Chem. / Year: 2013
Title: Structural, functional, and inhibition studies of a Gcn5-related N-acetyltransferase (GNAT) superfamily protein PA4794: a new C-terminal lysine protein acetyltransferase from pseudomonas aeruginosa.
Authors: Majorek, K.A. / Kuhn, M.L. / Chruszcz, M. / Anderson, W.F. / Minor, W.
History
DepositionApr 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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 PA4794
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6098
Polymers17,9031
Non-polymers1,7057
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.335, 76.121, 39.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein acetyltransferase PA4794


Mass: 17903.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: PA4794 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HV14
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-93M / (3R,5S,9R,26S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-10,14,20-trioxo-26-({[(phenylacetyl)amino]acetyl}amino)-2,4,6-trioxa-18-thia-11,15,21-triaza-3,5-diphosphaheptacosan-27-oic acid 3,5-dioxide (non-preferred name)


Mass: 1128.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H59N10O21P3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.38 Å3/Da / Density % sol: 48.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2M ammonium sulfate, 0.1M Bis Tris pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 4, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 34368 / % possible obs: 99.9 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.022 / Rrim(I) all: 0.057 / Χ2: 1.188 / Net I/σ(I): 9.8 / Num. measured all: 237096
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.426.80.816690.7770.330.8670.656100
1.42-1.456.80.6917000.8420.2840.7470.714100
1.45-1.486.90.55716800.8940.2280.6030.738100
1.48-1.516.90.46217150.9310.1890.50.715100
1.51-1.5470.42316810.9340.1720.4570.88100
1.54-1.5870.34216910.950.140.370.782100
1.58-1.6270.28117000.9680.1140.3030.811100
1.62-1.6670.23516810.9720.0960.2540.864100
1.66-1.7170.19417160.9830.0790.210.899100
1.71-1.7670.15917060.9870.0650.1710.98100
1.76-1.8370.13116900.9910.0530.1420.983100
1.83-1.970.10917150.9940.0440.1181.123100
1.9-1.9970.10217330.9940.0410.111.78499.9
1.99-2.096.90.07716960.9960.0320.0841.646100
2.09-2.226.90.06217200.9970.0250.0681.61299.8
2.22-2.396.90.0717430.9960.0290.0762.62699.9
2.39-2.636.90.04517330.9980.0190.0491.47899.7
2.63-3.026.90.03617580.9990.0150.0391.33199.8
3.02-3.86.80.0317630.9990.0120.0331.44299.8
3.8-506.30.03318780.9970.0140.0361.62799.1

-
Processing

Software
NameVersionClassification
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-3000data scaling
HKL-3000data reduction
HKL-3000phasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4L8A

4l8a


Resolution: 1.4→45.8 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1674 / WRfactor Rwork: 0.1434 / FOM work R set: 0.8717 / SU B: 2.039 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0603 / SU Rfree: 0.0538 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.06 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1704 1734 5.1 %RANDOM
Rwork0.1451 ---
obs0.1464 32591 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 108.08 Å2 / Biso mean: 20.311 Å2 / Biso min: 12.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2---0.62 Å20 Å2
3----0.99 Å2
Refinement stepCycle: final / Resolution: 1.4→45.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1233 0 131 188 1552
Biso mean--31.72 35.78 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191444
X-RAY DIFFRACTIONr_bond_other_d0.0010.021270
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9441979
X-RAY DIFFRACTIONr_angle_other_deg1.97232928
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3795168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.722.564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.70915208
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5691514
X-RAY DIFFRACTIONr_chiral_restr0.0770.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021733
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02313
X-RAY DIFFRACTIONr_rigid_bond_restr9.22731326
X-RAY DIFFRACTIONr_sphericity_free25.3095104
X-RAY DIFFRACTIONr_sphericity_bonded12.89951364
LS refinement shellResolution: 1.401→1.438 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 132 -
Rwork0.24 2300 -
all-2432 -
obs--98.3 %

+
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