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- PDB-2bl1: Crystal structure of a putative phosphinothricin Acetyltransferas... -

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Basic information

Entry
Database: PDB / ID: 2bl1
TitleCrystal structure of a putative phosphinothricin Acetyltransferase (PA4866) from Pseudomonas aeruginosa PAC1
ComponentsPUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE PA4866
KeywordsTRANSFERASE / GNAT / N-ACETYLTRANSFERASE / HYPOTHETICAL PROTEIN / PHOSPHINOTHRICIN / GCN5 FAMILY / PSEUDOMONAS AERUGINOSA
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / L-methionine sulfoximine/L-methionine sulfone acetyltransferase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsDavies, A.M. / Tata, R. / Agha, R. / Sutton, B.J. / Brown, P.R.
CitationJournal: Proteins: Struct., Funct., Bioinf. / Year: 2005
Title: Crystal Structure of a Putative Phosphinothricin Acetyltransferase (Pa4866) from Pseudomonas Aeruginosa Pac1
Authors: Davies, A.M. / Tata, R. / Agha, R. / Sutton, B.J. / Brown, P.R.
History
DepositionFeb 24, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 21, 2005Provider: 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 / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature
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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE PA4866
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4688
Polymers18,9201
Non-polymers5487
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)79.990, 79.990, 61.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PUTATIVE PHOSPHINOTHRICIN N-ACETYLTRANSFERASE PA4866


Mass: 18919.656 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAC1 (8602) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: Q9HUU7
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsIN STRAIN PAC1, RESIDUE 47 IS ALA, AS OPPOSED TO THR IN STRAIN PAO1 : SEQUENCE DISCREPANCY BETWEEN ...IN STRAIN PAC1, RESIDUE 47 IS ALA, AS OPPOSED TO THR IN STRAIN PAO1 : SEQUENCE DISCREPANCY BETWEEN PAC1 AND PAO1. RESIDUE 33 IS MODELLED AS ALA DUE TO DISORDER

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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: 2.23 Å3/Da / Density % sol: 44.39 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.3
Details: PROTEIN WAS CRYSTALLISED USING HANGING DROP VAPOUR DIFFUSION. RESERVOIR SOLUTION CONTAINED 1ML OF 0.1M HEPES AT PH7.3, 23-27% PEG 8000 AND 0.1% AZIDE. DROP SIZE WAS 1 MICROLITRE, TO WHICH 1 ...Details: PROTEIN WAS CRYSTALLISED USING HANGING DROP VAPOUR DIFFUSION. RESERVOIR SOLUTION CONTAINED 1ML OF 0.1M HEPES AT PH7.3, 23-27% PEG 8000 AND 0.1% AZIDE. DROP SIZE WAS 1 MICROLITRE, TO WHICH 1 MICROLITRE OF PROTEIN SOLUTION AT 10 MG/ML WAS ADDED.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 23, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 2→70 Å / Num. obs: 13388 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 12.8 % / Biso Wilson estimate: 21.11 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 96.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2→6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUES A 1 AND A 2 WERE DISORDERED AND THEREFORE NOT MODELLED
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 659 4.92 %RANDOM
Rwork0.1974 ---
obs0.1974 13388 96.1 %-
Solvent computationBsol: 61.36 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso mean: 24.04 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 6 Å / Luzzati sigma a obs: 0.18 Å
Refinement stepCycle: LAST / Resolution: 2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1303 0 35 213 1551
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
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_deg1.41
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.68
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
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
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 13 /
RfactorNum. reflection
Rfree0.2509 57
Rwork0.2656 954

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