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- PDB-1pea: AMIDE RECEPTOR/NEGATIVE REGULATOR OF THE AMIDASE OPERON OF PSEUDO... -

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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


regulation of amide catabolic process / amide binding / amino acid transport / kinase activity
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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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

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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

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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

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