[English] 日本語
Yorodumi
- PDB-2yep: STRUCTURE OF AN N-TERMINAL NUCLEOPHILE (NTN) HYDROLASE, OAT2, IN ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2yep
TitleSTRUCTURE OF AN N-TERMINAL NUCLEOPHILE (NTN) HYDROLASE, OAT2, IN COMPLEX WITH GLUTAMATE
Components
  • (GLUTAMATE N-ACETYLTRANSFERASE 2 BETA ...) x 2
  • GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
KeywordsTRANSFERASE / ACYL ENZYME / NTN HYDROLASE / ACYLTRANSFERASE / ORNITHINE ACETYL TRANSFERASE / HYDROLASE
Function / homology
Function and homology information


L-methionine N-acyltransferase activity / glutamate N-acetyltransferase / L-glutamate N-acetyltransferase activity, acting on acetyl-L-ornithine as donor / ornithine biosynthetic process / amino-acid N-acetyltransferase / clavulanic acid biosynthetic process / L-glutamate N-acetyltransferase activity / L-arginine biosynthetic process / cytoplasm
Similarity search - Function
arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) ...arginine biosynthesis bifunctional protein suprefamily / ArgJ beta chain, C-terminal domain / Arginine biosynthesis protein ArgJ / ArgJ beta chain, C-terminal domain / ArgJ family / arginine biosynthesis bifunctional protein fold / L-amino peptidase D-ALA esterase/amidase / L-amino peptidase D-ALA esterase/amidase / ArgJ-like domain superfamily / Ubiquitin-like (UB roll) / 4-Layer Sandwich / Roll / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / GLUTAMIC ACID / Glutamate N-acetyltransferase Oat2 / Arginine biosynthesis bifunctional protein ArgJ 3
Similarity search - Component
Biological speciesSTREPTOMYCES CLAVULIGERUS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsChowdhury, R. / Iqbal, A. / Clifton, I.J. / Schofield, C.J.
CitationJournal: Org.Biomol.Chem. / Year: 2011
Title: Structural and Biochemical Analyses Reveal How Ornithine Acetyl Transferase Binds Acidic and Basic Amino Acid Substrates.
Authors: Iqbal, A. / Clifton, I.J. / Chowdhury, R. / Ivison, D. / Domene, C. / Schofield, C.J.
History
DepositionMar 29, 2011Deposition site: PDBE / Processing site: PDBE
SupersessionSep 7, 2011ID: 2W4N
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_wavelength_list / _diffrn_source.source
Revision 2.0May 15, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Polymer sequence
Category: entity_poly / exptl_crystal_grow ...entity_poly / exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp ..._entity_poly.pdbx_seq_one_letter_code_can / _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_close_contact / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.type_symbol / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 3.1Dec 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,22512
Polymers166,8138
Non-polymers4124
Water7,548419
1
A: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
B: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8613
Polymers41,7142
Non-polymers1471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-33.6 kcal/mol
Surface area15900 Å2
MethodPISA
2
C: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
D: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,8613
Polymers41,7142
Non-polymers1471
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5910 Å2
ΔGint-43.3 kcal/mol
Surface area19260 Å2
MethodPISA
3
E: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
F: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7313
Polymers41,6722
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-33.3 kcal/mol
Surface area15050 Å2
MethodPISA
4
G: GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN
H: GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7733
Polymers41,7142
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-34 kcal/mol
Surface area15080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.220, 73.424, 172.327
Angle α, β, γ (deg.)90.00, 93.26, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.999829, -0.015048, -0.010744), (0.016346, 0.990947, 0.133252), (0.008641, -0.133405, 0.991024)-4.214, -25.932, -5.363
2given(0.790481, -0.031223, -0.61169), (-0.043143, -0.999057, -0.004757), (-0.610965, 0.030151, -0.791083)-19.115, 31.996, -68.116
3given(0.77566, -0.026282, -0.630604), (-0.094025, -0.992795, -0.074276), (-0.624108, 0.116905, -0.772543)-23.25, -3.657, -75.583
4given(0.99995, 0.00997, 0.000749), (-0.009984, 0.991762, 0.127707), (0.00053, -0.127708, 0.991812)-4.398, -26.011, -5.468
5given(0.806677, -0.006572, -0.590956), (-0.029791, -0.999119, -0.029553), (-0.590242, 0.041445, -0.806162)-19.985, 31.497, -68.94
6given(0.800696, -0.000496, -0.59907), (-0.076296, -0.991941, -0.101152), (-0.594192, 0.126699, -0.794282)-22.903, -4.505, -76.547

-
Components

-
Protein , 1 types, 4 molecules ACEG

#1: Protein
GLUTAMATE N-ACETYLTRANSFERASE 2 ALPHA CHAIN / ORNITHINE ACETYLTRANSFERASE 2 ALPHA CHAIN / ORNITHINE TRANSACETYLASE 2 ALPHA CHAIN / OATASE 2 ALPHA CHAIN


Mass: 18837.371 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase

-
GLUTAMATE N-ACETYLTRANSFERASE 2 BETA ... , 2 types, 4 molecules BDHF

#2: Protein GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE TRANSACETYLASE 2 BETA CHAIN / OATASE 2 BETA CHAIN


Mass: 22876.357 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase
#3: Protein GLUTAMATE N-ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE ACETYLTRANSFERASE 2 BETA CHAIN / ORNITHINE TRANSACETYLASE 2 BETA CHAIN / OATASE 2 BETA CHAIN


Mass: 22834.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Plasmid: PTYB12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q53940, UniProt: P0DJQ5*PLUS, glutamate N-acetyltransferase

-
Non-polymers , 3 types, 423 molecules

#4: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.4 %
Description: RMERGE AND REDUNDANCY VALUES NOT KNOWN, ESTIMATES GIVEN
Crystal growTemperature: 290 K / pH: 7.5
Details: 1.4M AMMONIUM SULPHATE, 100MM N-ACETYL -L-GLUTAMATE, 200MM NACL, 100MM TRIS HCL PH 7.5 .

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: OXFORD DIFFRACTION / Detector: CCD / Date: Nov 10, 2006 / Details: MULTI-LAYER OPTIC
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→61.12 Å / Num. obs: 60743 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 1 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.1
Reflection shell% possible all: 95.7

-
Processing

Software
NameVersionClassification
CNS1.1refinement
CrysalisProdata reduction
CrysalisProdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VZ6, CHAIN A

1vz6


Resolution: 2.7→61.12 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 3620114.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2209 5.4 %RANDOM
Rwork0.218 ---
obs0.218 40637 96 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.54 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å2-0.43 Å2
2--1.1 Å20 Å2
3----0.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.07 Å
Refinement stepCycle: LAST / Resolution: 2.7→61.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11206 0 26 419 11651
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.7→2.77 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.236 156 5.1 %
Rwork0.223 2916 -
obs--95.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2TH5.PARTH5.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5ACT.PARACT.TOP

+
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