[English] 日本語
Yorodumi
- PDB-1pea: AMIDE RECEPTOR/NEGATIVE REGULATOR OF THE AMIDASE OPERON OF PSEUDO... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pea
TitleAMIDE RECEPTOR/NEGATIVE REGULATOR OF THE AMIDASE OPERON OF PSEUDOMONAS AERUGINOSA (AMIC) COMPLEXED WITH ACETAMIDE
ComponentsAMIDASE OPERON
KeywordsBINDING PROTEIN / GENE REGULATOR / RECEPTOR
Function / homology
Function and homology information


amide binding / regulation of amide catabolic process / amino acid transport / kinase activity / phosphorylation
Similarity search - Function
AmiC, periplasmic binding domain / Periplasmic binding protein domain / Leu/Ile/Val-binding protein / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETAMIDE / Aliphatic amidase expression-regulating protein
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsPearl, L.H. / O'Hara, B.P.
Citation
Journal: EMBO J. / Year: 1994
Title: Crystal structure of AmiC: the controller of transcription antitermination in the amidase operon of Pseudomonas aeruginosa.
Authors: Pearl, L. / O'Hara, B. / Drew, R. / Wilson, S.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary X-Ray Data for the Negative Regulator (Amic) of the Amidase Operon of Pseudomonas Aeruginosa
Authors: Wilson, S.A. / Chayen, N.E. / Hemmings, A.M. / Drew, R.E. / Pearl, L.H.
#2: Journal: Embo J. / Year: 1993
Title: Antitermination of Amidase Expression in Pseudomonas Aeruginosa is Controlled by a Novel Cytoplasmic Amide-Binding Protein
Authors: Wilson, S.A. / Wachira, S.J. / Drew, R.E. / Jones, D. / Pearl, L.H.
History
DepositionNov 16, 1995Processing site: BNL
Revision 1.0Apr 3, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.process_site / _struct_ref_seq_dif.details / _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: AMIDASE OPERON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0192
Polymers42,9601
Non-polymers591
Water2,288127
1
A: AMIDASE OPERON
hetero molecules

A: AMIDASE OPERON
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,0384
Polymers85,9202
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)104.960, 104.960, 65.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein AMIDASE OPERON


Mass: 42960.031 Da / Num. of mol.: 1 / Fragment: AMIDE RECEPTOR/NEGATIVE REGULATOR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAC1 / Production host: Pseudomonas aeruginosa (bacteria) / References: UniProt: P27017
#2: Chemical ChemComp-ACM / ACETAMIDE / Acetamide


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.11 Å3/Da / Density % sol: 41.65 %
Crystal
*PLUS
Density % sol: 43 %
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion / Details: macro-seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
112 mg/mlAmiC1drop
26 %(w/v)PEG40001drop
320 mMTris-HCl1drop
4150 mMammonium sulfate1drop

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.882 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.882 Å / Relative weight: 1
ReflectionResolution: 2.1→8 Å / Num. obs: 21687 / % possible obs: 96 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.064
Reflection
*PLUS
Rmerge(I) obs: 0.101

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.1→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.275 -5 %
Rwork0.206 --
obs0.206 20650 -
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 4 127 3045
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_improper_angle_deg1.8

+
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