[English] 日本語
Yorodumi
- PDB-3d8p: Crystal structure of acetyltransferase of GNAT family (NP_373092.... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d8p
TitleCrystal structure of acetyltransferase of GNAT family (NP_373092.1) from STAPHYLOCOCCUS AUREUS MU50 at 2.20 A resolution
Componentsacetyltransferase of GNAT family
KeywordsTRANSFERASE / NP_373092.1 / acetyltransferase of GNAT family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Acetyltransferase (GNAT) family
Function / homology
Function and homology information


N-acetyltransferase activity / metal ion binding
Similarity search - Function
: / 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
ACETATE ION / N-acetyltransferase domain-containing protein / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of acetyltransferase of GNAT family (NP_373092.1) from STAPHYLOCOCCUS AUREUS MU50 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 9, 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: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.6Oct 22, 2025Group: Structure summary / Category: audit_author

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: acetyltransferase of GNAT family
B: acetyltransferase of GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,55117
Polymers38,6512
Non-polymers90015
Water4,107228
1
A: acetyltransferase of GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6707
Polymers19,3251
Non-polymers3446
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: acetyltransferase of GNAT family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,88110
Polymers19,3251
Non-polymers5569
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.597, 135.597, 103.578
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-356-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAILEILE5AA2 - 33 - 4
21ALAALAILEILE5BB2 - 33 - 4
12ASNASNPHEPHE2AA4 - 1345 - 135
22ASNASNPHEPHE2BB4 - 1345 - 135
13PHEPHELYSLYS2AA155 - 161156 - 162
23PHEPHELYSLYS2BB155 - 161156 - 162
DetailsAUTHORS STATE THAT THE RESULTS FROM SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein acetyltransferase of GNAT family


Mass: 19325.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Gene: NP_373092.1, SAV2568 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q99R70, UniProt: A0A0H3JTS0*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 24.0% polyethylene glycol 3350, 0.186M calcium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97867 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97867 Å / Relative weight: 1
ReflectionResolution: 2.2→28.364 Å / Num. obs: 24768 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 37.319 Å2 / Rmerge(I) obs: 0.127 / Rrim(I) all: 0.137 / Rsym value: 0.127 / Net I/σ(I): 5.146 / Num. measured all: 182046
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) allMean I/σ(I) obsNum. measured allNum. unique allRrim(I) allRsym value% possible all
2.2-2.267.40.8822.30.91337918020.9480.882100
2.26-2.327.40.782.611319317720.8380.78100
2.32-2.397.40.6353.21.21259116970.6820.635100
2.39-2.467.40.5443.81.41239716670.5850.544100
2.46-2.547.50.4754.31.61201616120.510.475100
2.54-2.637.40.3925.221159315570.4210.392100
2.63-2.737.40.3186.52.41125315200.3420.318100
2.73-2.847.40.2438.53.21079314490.2610.243100
2.84-2.977.40.19610.33.91037013980.210.196100
2.97-3.117.40.15113.251006013570.1620.151100
3.11-3.287.40.11816.36.4931012600.1270.118100
3.28-3.487.40.10119.77.2902512240.1080.101100
3.48-3.727.30.08624.68830211360.0930.086100
3.72-4.027.30.07429.49.1782910680.080.074100
4.02-4.47.30.06931.69.371959920.0750.069100
4.4-4.927.30.06234.310.365479020.0660.062100
4.92-5.687.10.06830.89.457338060.0730.068100
5.68-6.967.10.07628.7948106810.0820.076100
6.96-9.846.80.06336.49.337365510.0680.063100
9.84-28.3660.05539.710.519143170.060.05596

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→28.364 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 9.007 / SU ML: 0.121 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.172
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.CALCIUM, ACETATE IONS FROM CRYSTALLIZATION AND ETHYLENE GLYCOL MOLECULES FROM CRYO CONDITION ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1260 5.1 %RANDOM
Rwork0.172 23508 --
obs0.174 24768 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.66 Å2 / Biso mean: 35.917 Å2 / Biso min: 15.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2602 0 57 228 2887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222734
X-RAY DIFFRACTIONr_bond_other_d0.0010.021906
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9593659
X-RAY DIFFRACTIONr_angle_other_deg0.95134624
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7365324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78624.966147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98115495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6921516
X-RAY DIFFRACTIONr_chiral_restr0.0910.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023036
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined0.2190.2521
X-RAY DIFFRACTIONr_nbd_other0.1920.21975
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21328
X-RAY DIFFRACTIONr_nbtor_other0.0850.21411
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2820.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.215
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.190.22
X-RAY DIFFRACTIONr_mcbond_it1.87431690
X-RAY DIFFRACTIONr_mcbond_other0.4793658
X-RAY DIFFRACTIONr_mcangle_it2.69152595
X-RAY DIFFRACTIONr_scbond_it4.53481223
X-RAY DIFFRACTIONr_scangle_it5.993111064
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
788TIGHT POSITIONAL0.220.15
1067MEDIUM POSITIONAL0.51
8LOOSE POSITIONAL0.455
788TIGHT THERMAL0.461
1067MEDIUM THERMAL1.64
8LOOSE THERMAL2.1610
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 89 -
Rwork0.214 1713 -
all-1802 -
obs--100 %
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)
12.07810.8061-1.66021.5345-0.93693.7855-0.0780.1264-0.14670.0582-0.0042-0.01910.1893-0.32370.0822-0.0999-0.02090.0154-0.0016-0.0172-0.075315.910534.46116.0722
22.48220.01-0.71020.4833-0.07431.33140.060.17410.0688-0.0271-0.0486-0.1514-0.1370.1372-0.0114-0.1075-0.01240.0257-0.0459-0.0073-0.0734-12.261733.182241.8615
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 1613 - 162
2X-RAY DIFFRACTION2BB2 - 1613 - 162

+
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