[English] 日本語
Yorodumi
- PDB-4c5p: The structure of mycobacterium marinum arylamine n-acetyltransferase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4c5p
TitleThe structure of mycobacterium marinum arylamine n-acetyltransferase
ComponentsARYLAMINE N-ACETYLTRANSFERASE
KeywordsTRANSFERASE / TUBERCULOSIS
Function / homology
Function and homology information


acetyltransferase activity
Similarity search - Function
Arylamine N-acetyltransferase / Cysteine proteinases / Arylamine N-acetyltransferase fold / Arylamine N-acetyltransferase / N-acetyltransferase / Papain-like cysteine peptidase superfamily / Lipocalin / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Arylamine N-acetyltransferase Nat
Similarity search - Component
Biological speciesMYCOBACTERIUM MARINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.592 Å
AuthorsAbuhammad, A. / Lowe, E.D. / Garman, E.F. / Sim, E.
CitationJournal: Ph D Thesis
Title: Arylamine N-Acetyltransferases from Mycobacteria: Investigations of a Potential Target for Anti- Tubercular Therapy
Authors: Abuhammad, A.
History
DepositionSep 13, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Atomic model
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ARYLAMINE N-ACETYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2395
Polymers30,9671
Non-polymers2724
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.750, 51.750, 176.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2221-

HOH

-
Components

#1: Protein ARYLAMINE N-ACETYLTRANSFERASE


Mass: 30967.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM MARINUM (bacteria) / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: B2HIZ6, arylamine N-acetyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1.87 Å3/Da / Density % sol: 34.3 % / Description: NONE
Crystal growDetails: 0.2 M NA2SO4, 0.1 M BIS-TRIS PROPANE PH 6.5 AND 20 % W/V PEG-3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 1.59→38.8 Å / Num. obs: 33245 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 6.7 % / Biso Wilson estimate: 17.11 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.7

-
Processing

SoftwareName: PHENIX / Version: (PHENIX.REFINE) / Classification: refinement
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 1.592→38.82 Å / SU ML: 0.16 / σ(F): 1.36 / Phase error: 16.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1935 1675 5.1 %
Rwork0.1545 --
obs0.1564 33153 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.7 Å2
Refinement stepCycle: LAST / Resolution: 1.592→38.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2062 0 17 284 2363
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012233
X-RAY DIFFRACTIONf_angle_d1.2833057
X-RAY DIFFRACTIONf_dihedral_angle_d13.532800
X-RAY DIFFRACTIONf_chiral_restr0.077350
X-RAY DIFFRACTIONf_plane_restr0.006404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.592-1.63890.28361390.2582554X-RAY DIFFRACTION100
1.6389-1.69180.28011590.22982546X-RAY DIFFRACTION100
1.6918-1.75230.22421370.21572568X-RAY DIFFRACTION100
1.7523-1.82240.2341350.18272576X-RAY DIFFRACTION100
1.8224-1.90540.20521390.15832576X-RAY DIFFRACTION100
1.9054-2.00580.16951270.13292612X-RAY DIFFRACTION100
2.0058-2.13150.16171330.12942597X-RAY DIFFRACTION100
2.1315-2.2960.19381600.12572590X-RAY DIFFRACTION100
2.296-2.5270.17821390.13512625X-RAY DIFFRACTION100
2.527-2.89260.17331320.142666X-RAY DIFFRACTION100
2.8926-3.64390.16391410.13992692X-RAY DIFFRACTION100
3.6439-38.83110.20951340.1662876X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 22.349 Å / Origin y: 1.1728 Å / Origin z: 12.1545 Å
111213212223313233
T0.0651 Å20.01 Å2-0.0022 Å2-0.055 Å2-0.0006 Å2--0.0435 Å2
L0.8541 °2-0 °2-0.0026 °2-0.8879 °2-0.1175 °2--0.8455 °2
S0.007 Å °-0.0763 Å °-0.0268 Å °0.0606 Å °0.0047 Å °-0.0469 Å °0.0465 Å °0.0603 Å °-0.0101 Å °
Refinement TLS groupSelection details: ALL

+
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