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

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Basic information

Entry
Database: PDB / ID: 1qnl
TitleAMIDE RECEPTOR/NEGATIVE REGULATOR OF THE AMIDASE OPERON OF PSEUDOMONAS AERUGINOSA (AMIC) COMPLEXED WITH BUTYRAMIDE
ComponentsALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN
KeywordsTRANSFERASE / BINDING PROTEIN / GENE REGULATOR / RECEPTOR / KINASE / REPRESSOR
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
BUTYRAMIDE / Aliphatic amidase expression-regulating protein
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPearl, L.H. / O'Hara, B.P. / Roe, S.M.
Citation
Journal: Protein Eng. / Year: 2000
Title: Structural Adaptation to Selective Pressure for Altered Ligand Specificity in the Pseudomonas Aeruginosa Amide Receptor, Amic
Authors: O'Hara, B.P. / Wilson, S.A. / Lee, A.W.L. / Roe, S.M. / Siligardi, G. / 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.A.
#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 19, 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 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / struct_biol / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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: ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0602
Polymers42,9731
Non-polymers871
Water77543
1
A: ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN
hetero molecules

A: ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN
hetero molecules

A: ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN
hetero molecules

A: ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,2418
Polymers171,8924
Non-polymers3484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation7_555y,x,-z1
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.150, 104.150, 65.680
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 ALIPHATIC AMIDASE EXPRESSION-REGULATING PROTEIN / AMIC


Mass: 42973.027 Da / Num. of mol.: 1 / Fragment: AMIDE RECEPTOR/NEGATIVE REGULATOR, RESIDUES 7-374
Source method: isolated from a genetically manipulated source
Details: BUTYRAMIDE COMPLEX / Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAC1 / Production host: PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P27017
#2: Chemical ChemComp-BMD / BUTYRAMIDE


Mass: 87.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSWISSPROT HAS THE WRONG SEQUENCE, STRUCTURE IS CORRECT. GLN 27 UNP P27017 HIS 26 ARG 28 UNP P27017 ALA 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growMethod: microbatch / pH: 7
Details: MICROBATCH CRYSTALLISATION. WELLS CONTAIN 12.8MG/ML PAC181-AMIC, 5MM BUTYRAMIDE, 1.36M NA CITRATE, 100MM HEPES-NAOH PH7.5, pH 7.00
Crystal grow
*PLUS
Method: other / Details: Chayen, N.E., (1992) J. Crystal Growth, 122, 176.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→38 Å / Num. obs: 10389 / % possible obs: 97.8 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 54.2 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 4.5
Reflection shellResolution: 2.7→2.84 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 3.8 / % possible all: 97.2
Reflection shell
*PLUS
% possible obs: 97.2 %

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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: 2.7→15 Å / SU B: 16.04 / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.47
Details: RESIDUES 2 - 7, 40 - 50, 222 - 226, 347 - 349 AND 376 - 385 IN THIS MOLECULE ARE NOT DEFINED IN THE ELECTRON DENSITY AND ARE PRESUMED TO BE DISORDERED. THERE ARE ALSO A FEW OTHER RESIDUES ...Details: RESIDUES 2 - 7, 40 - 50, 222 - 226, 347 - 349 AND 376 - 385 IN THIS MOLECULE ARE NOT DEFINED IN THE ELECTRON DENSITY AND ARE PRESUMED TO BE DISORDERED. THERE ARE ALSO A FEW OTHER RESIDUES THAT COULD NOT BE SATISFACTORILY REFINED, NAMELY: 37, 68, 72, 74, 137, 165, 194, 195, 261, 307, 318, 319, 328, 359. SOME OF THIS ARE MISSING MAIN CHAIN AS WELL AS SIDE CHAIN ATOMS.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 477 5 %RANDOM
Rwork0.269 ---
obs-9546 97 %-
Displacement parametersBiso mean: 27.38 Å2
Refinement stepCycle: LAST / Resolution: 2.7→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 6 43 2963
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0290.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.972
X-RAY DIFFRACTIONp_mcangle_it1.6652.5
X-RAY DIFFRACTIONp_scbond_it1.9673
X-RAY DIFFRACTIONp_scangle_it3.0124.5
X-RAY DIFFRACTIONp_plane_restr0.0166
X-RAY DIFFRACTIONp_chiral_restr0.0990.15
X-RAY DIFFRACTIONp_singtor_nbd0.1930.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1810.3
X-RAY DIFFRACTIONp_planar_tor2.87
X-RAY DIFFRACTIONp_staggered_tor20.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.420
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS

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