[English] 日本語
Yorodumi
- PDB-4e2a: Crystal Structure of the Putative acetyltransferase from Streptoc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4e2a
TitleCrystal Structure of the Putative acetyltransferase from Streptococcus mutans
ComponentsPutative acetyltransferase
KeywordsTRANSFERASE / Alpha Beta / Alpha and Beta Proteins (a+b) / N-acetyltransferase activity
Function / homology
Function and homology information


N-acetyltransferase activity
Similarity search - Function
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
Putative acetyltransferase
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLi, G.L. / Nie, J.K. / Li, L.F. / Su, X.D.
Citation
Journal: To be Published
Title: Crystal Structure of the Putative acetyltransferase from Streptococcus mutans
Authors: Li, G.L. / Nie, J.K. / Li, L.F. / Su, X.D.
#1: Journal: Biochem.Biophys.Res.Commun. / Year: 2009
Title: Solid-liquid interface method (SLIM): a new crystallization method for proteins.
Authors: Brostromer, E. / Nan, J. / Li, L.F. / Su, X.D.
#2: Journal: J.Biol.Chem. / Year: 2005
Title: Structural and functional evidence for Bacillus subtilis PaiA as a novel N1-spermidine/spermine acetyltransferase.
Authors: Forouhar, F. / Lee, I.S. / Vujcic, J. / Vujcic, S. / Shen, J. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Porter, C.W. / Tong, L.
History
DepositionMar 8, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative acetyltransferase
B: Putative acetyltransferase


Theoretical massNumber of molelcules
Total (without water)47,2132
Polymers47,2132
Non-polymers00
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-10 kcal/mol
Surface area17990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.700, 75.700, 80.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 3 - 172 / Label seq-ID: 37 - 206

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN A AND (RESSEQ 3:172)AA
2CHAIN B AND (RESSEQ 3:172)BB

-
Components

#1: Protein Putative acetyltransferase /


Mass: 23606.742 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: SMU_1511c / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 / References: UniProt: Q8DT67
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.45 Å3/Da / Density % sol: 49.89 %
Crystal growTemperature: 289.2 K / Method: solid-liquid interface method / pH: 7
Details: 0.2M Magnesium formate, 20% PEG 3350, pH 7.0, SOLID-LIQUID INTERFACE METHOD, temperature 289.2K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 29, 2010
RadiationMonochromator: TOROIDAL MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 30907 / % possible obs: 95.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 18.4 % / Rmerge(I) obs: 0.066 / Rsym value: 0.087 / Net I/σ(I): 22.83
Reflection shellResolution: 2→2.1 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 6.21 / Num. unique all: 2192 / Rsym value: 0.485 / % possible all: 100

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TIQ

1tiq


Resolution: 2→18.996 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.809 / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 26.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2405 1465 4.97 %RANDOM
Rwork0.2148 ---
obs0.2162 29476 95.5 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 25.887 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso max: 94.08 Å2 / Biso mean: 33.8687 Å2 / Biso min: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.6787 Å2-0 Å20 Å2
2---0.6787 Å2-0 Å2
3---1.3575 Å2
Refinement stepCycle: LAST / Resolution: 2→18.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2804 0 0 250 3054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092864
X-RAY DIFFRACTIONf_angle_d1.123858
X-RAY DIFFRACTIONf_chiral_restr0.105417
X-RAY DIFFRACTIONf_plane_restr0.003485
X-RAY DIFFRACTIONf_dihedral_angle_d14.0861032
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1399X-RAY DIFFRACTIONPOSITIONAL0.037
12B1399X-RAY DIFFRACTIONPOSITIONAL0.037
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07140.28821590.243629003059100
2.0714-2.15430.28791340.246129303064100
2.1543-2.25220.39851190.32812348246780
2.2522-2.37070.40521130.34342296240978
2.3707-2.51890.26711720.227729213093100
2.5189-2.71290.2791500.24529043054100
2.7129-2.98490.28411540.23129343088100
2.9849-3.41470.20581650.203629253090100
3.4147-4.29390.17891410.18342879302097
4.2939-18.99710.20381580.170329743132100

+
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