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- PDB-1qo0: Amide receptor of the amidase operon of Pseudomonas aeruginosa (A... -

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Basic information

Entry
Database: PDB / ID: 1qo0
TitleAmide receptor of the amidase operon of Pseudomonas aeruginosa (AmiC) complexed with the negative regulator AmiR.
Components
  • AMIC
  • AMIR
KeywordsBINDING PROTEIN / GENE REGULATOR / RECEPTOR
Function / homology
Function and homology information


amide binding / regulation of amide catabolic process / cellular catabolic process / positive regulation of hydrolase activity / carbon utilization / amino acid transport / transcription antitermination / kinase activity / phosphorylation / RNA binding
Similarity search - Function
AmiC, periplasmic binding domain / Periplasmic binding protein domain / Signal transduction response regulator, antiterminator / ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / Leu/Ile/Val-binding protein / CheY-like superfamily / Response regulator ...AmiC, periplasmic binding domain / Periplasmic binding protein domain / Signal transduction response regulator, antiterminator / ANTAR domain / ANTAR domain / ANTAR domain profile. / ANTAR / Leu/Ile/Val-binding protein / CheY-like superfamily / Response regulator / Periplasmic binding protein-like I / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BUTYRAMIDE / Aliphatic amidase regulator / Aliphatic amidase expression-regulating protein
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsPearl, L.H. / O'Hara, B.P. / Roe, S.M.
Citation
Journal: Embo J. / Year: 1999
Title: Crystal Structure and Induction Mechanism of Amic-Amir: A Ligand-Regulated Transcription Antitermination Complex
Authors: O'Hara, B.P. / Norman, R.A. / Wan, P.T.C. / Roe, S.M. / Barrett, T.E. / Drew, R.E. / Pearl, L.H.
#1: 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.H. / O'Hara, B.P. / Drew, R.E. / Wilson, S.W.
#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.
#3: 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.
History
DepositionOct 26, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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: AMIC
B: AMIC
D: AMIR
E: AMIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,9016
Polymers129,7274
Non-polymers1742
Water15,331851
1
A: AMIC
B: AMIC
D: AMIR
E: AMIR
hetero molecules

A: AMIC
B: AMIC
D: AMIR
E: AMIR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,80212
Polymers259,4538
Non-polymers3484
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area21060 Å2
ΔGint-124.2 kcal/mol
Surface area104380 Å2
MethodPQS
Unit cell
Length a, b, c (Å)308.440, 67.150, 76.410
Angle α, β, γ (deg.)90.00, 103.33, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein AMIC


Mass: 42960.031 Da / Num. of mol.: 2 / Fragment: AMIDE RECEPTOR
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH BUTYRAMIDE MOLECULE / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAC1 / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P27017
#2: Protein AMIR


Mass: 21903.287 Da / Num. of mol.: 2 / 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: P10932
#3: Chemical ChemComp-BMD / BUTYRAMIDE / Butyramide


Mass: 87.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H9NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSWISSPROT HAS THE WRONG SEQUENCE, STRUCTURE IS CORRECT. CHAINS A AND B GLN 27 SWS P27017 HIS 26 ARG ...SWISSPROT HAS THE WRONG SEQUENCE, STRUCTURE IS CORRECT. CHAINS A AND B GLN 27 SWS P27017 HIS 26 ARG 28 SWS P27017 ALA 27 CHAINS D AND E ARG 64 SWS P10932 GLY 27

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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: 2.96 Å3/Da / Density % sol: 58 %
Crystal growMethod: microbatch / pH: 5.6
Details: CRYSTALLISATION WAS BY MICRO-BATCH AND STREAK SEEDING. WELLS CONTAINED 8-8.5% PEG4000, 20%(V/V) 2-PROPANOL, 50MM SODIUM CITRATE BUFFERED AT PH 5.6 AND AMIC-AMIR COMPLEX AT 5MG/ML (FINAL CONCENTRATION).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.25→33.6 Å / Num. obs: 67099 / % possible obs: 83.8 % / Redundancy: 2.7 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.052 / Net I/σ(I): 6.8
Reflection shellResolution: 2.25→2.36 Å / Redundancy: 1.5 % / Mean I/σ(I) obs: 3 / Rsym value: 0.177 / % possible all: 69.3

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Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PEA

1pea


Resolution: 2.25→20 Å / SU B: 6.63 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.24
RfactorNum. reflection% reflectionSelection details
Rfree0.256 3055 5 %RANDOM
Rwork0.186 ---
obs-62185 83 %-
Displacement parametersBiso mean: 9.48 Å2
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8798 0 12 851 9661
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3052
X-RAY DIFFRACTIONp_mcangle_it2.0512.5
X-RAY DIFFRACTIONp_scbond_it33
X-RAY DIFFRACTIONp_scangle_it4.2984.5
X-RAY DIFFRACTIONp_plane_restr0.022
X-RAY DIFFRACTIONp_chiral_restr0.1220.15
X-RAY DIFFRACTIONp_singtor_nbd0.1850.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd00.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.1550.3
X-RAY DIFFRACTIONp_planar_tor6.87
X-RAY DIFFRACTIONp_staggered_tor18.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.220
X-RAY DIFFRACTIONp_special_tor015

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