[English] 日本語
Yorodumi
- PDB-3g3s: Crystal structure of GCN5-related N-acetyltransferase-like protei... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3g3s
TitleCrystal structure of GCN5-related N-acetyltransferase-like protein (ZP_00874857) (ZP_00874857.1) from Streptococcus suis 89/1591 at 1.80 A resolution
ComponentsGCN5-related N-acetyltransferase
KeywordsTRANSFERASE / ZP_00874857.1 / GCN5-related N-acetyltransferase-like protein (ZP_00874857) / Acetyltransferase (GNAT) family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyGNAT acetyltransferase-like / Gcn5-related N-acetyltransferase (GNAT) / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta / CACODYLATE ION / :
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of GCN5-related N-acetyltransferase-like protein (ZP_00874857) (ZP_00874857.1) from Streptococcus suis 89/1591 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 2, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / 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 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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 / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GCN5-related N-acetyltransferase
B: GCN5-related N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,34510
Polymers56,8132
Non-polymers5328
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.395, 83.880, 93.763
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein GCN5-related N-acetyltransferase


Mass: 28406.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 89/1591 / Gene: SsuiDRAFT_1367, ZP_00874857.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q302C5
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.20M MgCl2, 10.0% PEG 3000, 0.1M Cacodylate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162, 0.97821, 0.97879
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 15, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.978211
30.978791
ReflectionResolution: 1.8→29.285 Å / Num. obs: 52108 / % possible obs: 98.8 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.743 Å2 / Rmerge(I) obs: 0.108 / Rsym value: 0.108 / Net I/σ(I): 4.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.853.70.75311391837610.75398
1.85-1.93.70.6461.21371736960.64698.1
1.9-1.953.70.521.51325335730.5298.1
1.95-2.013.70.4291.81293834900.42998.6
2.01-2.083.70.3322.31256933940.33298.5
2.08-2.153.70.2792.71217632740.27998.3
2.15-2.233.70.2393.11192532020.23998.9
2.23-2.323.70.1963.81142730610.19698.7
2.32-2.433.70.1684.31094629350.16899
2.43-2.553.70.1544.71062528480.15498.9
2.55-2.683.70.1295.51007527120.12999.3
2.68-2.853.70.1076.3949625590.10799
2.85-3.043.70.0866.8880823890.08699.3
3.04-3.293.70.0727.8833922780.07299.3
3.29-3.63.60.0628.1760520930.06299.4
3.6-4.023.60.0567.6688419000.05699.3
4.02-4.653.60.0499.4610816950.04999.5
4.65-5.693.50.0499.7512714470.04999.6
5.69-8.053.50.04812.8396211470.04899.7
8.05-29.2853.20.04511.621256540.04596.9

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.285 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 4.731 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.143 / ESU R Free: 0.134
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. CACODYLATE ANION, NA ION AND ETHYLENE GLYCOL FROM CRYSTALLIZATION AND CRYOPROTECTANT ARE MODELED INTO THIS STRUCTURE, RESPECTIVELY.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 2652 5.1 %RANDOM
Rwork0.203 ---
obs0.205 52068 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 77.16 Å2 / Biso mean: 32.395 Å2 / Biso min: 6 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2---2.07 Å20 Å2
3---4.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3904 0 30 532 4466
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224101
X-RAY DIFFRACTIONr_bond_other_d0.0020.022727
X-RAY DIFFRACTIONr_angle_refined_deg1.5761.9635567
X-RAY DIFFRACTIONr_angle_other_deg0.96536633
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9035516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54624.316190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64215672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.261523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2605
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024660
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02862
X-RAY DIFFRACTIONr_nbd_refined0.1990.3899
X-RAY DIFFRACTIONr_nbd_other0.1690.33039
X-RAY DIFFRACTIONr_nbtor_refined0.1870.51992
X-RAY DIFFRACTIONr_nbtor_other0.090.52168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.5652
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0540.51
X-RAY DIFFRACTIONr_metal_ion_refined0.0410.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.337
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.529
X-RAY DIFFRACTIONr_mcbond_it1.81432520
X-RAY DIFFRACTIONr_mcbond_other0.47231044
X-RAY DIFFRACTIONr_mcangle_it3.00454027
X-RAY DIFFRACTIONr_scbond_it5.26681654
X-RAY DIFFRACTIONr_scangle_it7.52111540
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 185 -
Rwork0.345 3571 -
all-3756 -
obs--97.66 %

+
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