[English] 日本語
Yorodumi
- PDB-5jph: Structure of a GNAT acetyltransferase SACOL1063 from Staphylococc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jph
TitleStructure of a GNAT acetyltransferase SACOL1063 from Staphylococcus aureus in complex with CoA
ComponentsAcetyltransferase SACOL1063
KeywordsTRANSFERASE / acetyltransferase / Gcn5-related N-acetyltransferase / GNAT / protein acetylation / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


glucosamine 6-phosphate N-acetyltransferase activity / acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Glucosamine 6-phosphate N-acetyltransferase / Acetyltransferase (GNAT) domain / 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
COENZYME A / Acetyltransferase SACOL1063
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.46 Å
AuthorsMajorek, K.A. / Osinski, T. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Biochim.Biophys.Acta / Year: 2016
Title: Insight into the 3D structure and substrate specificity of previously uncharacterized GNAT superfamily acetyltransferases from pathogenic bacteria.
Authors: Majorek, K.A. / Osinski, T. / Tran, D.T. / Revilla, A. / Anderson, W.F. / Minor, W. / Kuhn, M.L.
History
DepositionMay 3, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Dec 7, 2016Group: Other
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acetyltransferase SACOL1063
B: Acetyltransferase SACOL1063
C: Acetyltransferase SACOL1063
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,62512
Polymers50,9133
Non-polymers4,7129
Water11,638646
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8370 Å2
ΔGint-28 kcal/mol
Surface area20610 Å2
2
A: Acetyltransferase SACOL1063
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5424
Polymers16,9711
Non-polymers1,5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-7 kcal/mol
Surface area7410 Å2
MethodPISA
3
B: Acetyltransferase SACOL1063
hetero molecules

C: Acetyltransferase SACOL1063
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0838
Polymers33,9422
Non-polymers3,1416
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_558-x,y+1/2,-z+31
Buried area5500 Å2
ΔGint-22 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.088, 93.821, 68.910
Angle α, β, γ (deg.)90.000, 97.150, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALALEULEUAA0 - 1403 - 143
21ALAALALEULEUBB0 - 1403 - 143
12ALAALALEULEUAA0 - 1403 - 143
22ALAALALEULEUCC0 - 1403 - 143
13SERSERTHRTHRBB-2 - 1411 - 144
23SERSERTHRTHRCC-2 - 1411 - 144

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein Acetyltransferase SACOL1063 / GCN5-related N-acetyltransferase / GNAT


Mass: 16970.990 Da / Num. of mol.: 3 / Mutation: V28I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: COL / Gene: SACOL1063 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5HH30, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 646 / 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: 3.16 Å3/Da / Density % sol: 61.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Bis-tris propane pH 7.0 and 2.2 M DL-Malic acid

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 8, 2013 / Details: mirrors
RadiationMonochromator: Si [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 108551 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/av σ(I): 36.747 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.46-1.494.60.6722.1198.3
1.49-1.514.80.547198.4
1.51-1.544.80.458198.6
1.54-1.574.80.369198.9
1.57-1.614.80.332198.8
1.61-1.644.80.29198.7
1.64-1.694.80.238199.1
1.69-1.734.80.203199.2
1.73-1.784.80.162199.2
1.78-1.844.80.135199.2
1.84-1.914.80.116199.6
1.91-1.984.80.096199.6
1.98-2.074.80.08199.7
2.07-2.184.80.069199.8
2.18-2.324.80.067199.9
2.32-2.54.80.065199.9
2.5-2.754.70.0641100
2.75-3.154.70.0571100
3.15-3.964.60.039199.8
3.96-504.50.041194.6

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.46→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.738 / SU ML: 0.035 / SU R Cruickshank DPI: 0.0565 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.056 / ESU R Free: 0.054
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1697 5418 5 %RANDOM
Rwork0.1417 ---
obs0.1431 102969 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 73.2 Å2 / Biso mean: 22.71 Å2 / Biso min: 11.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0.29 Å2
2--0.29 Å2-0 Å2
3----0.21 Å2
Refinement stepCycle: final / Resolution: 1.46→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3432 0 291 647 4370
Biso mean--28.79 36.26 -
Num. residues----430
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194148
X-RAY DIFFRACTIONr_bond_other_d0.0050.023869
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9845651
X-RAY DIFFRACTIONr_angle_other_deg1.77138968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0915498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.23524.785186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.90115664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3961524
X-RAY DIFFRACTIONr_chiral_restr0.0980.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024991
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02921
X-RAY DIFFRACTIONr_mcbond_it1.7362.2681900
X-RAY DIFFRACTIONr_mcbond_other1.7492.1741899
X-RAY DIFFRACTIONr_mcangle_it2.1662421
X-RAY DIFFRACTIONr_rigid_bond_restr8.64233813
X-RAY DIFFRACTIONr_sphericity_bonded11.23153725
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A178380.08
12B178380.08
21A174680.1
22C174680.1
31B175500.1
32C175500.1
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 388 -
Rwork0.231 7545 -
all-7933 -
obs--98.41 %

+
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