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- PDB-2vi7: Structure of a Putative Acetyltransferase (PA1377)from Pseudomona... -

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Basic information

Entry
Database: PDB / ID: 2vi7
TitleStructure of a Putative Acetyltransferase (PA1377)from Pseudomonas aeruginosa
ComponentsACETYLTRANSFERASE PA1377
KeywordsTRANSFERASE / GNAT / GCN5 FAMILY / N-ACETYLTRANSFERASE / HYPOTHETICAL PROTEIN
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl 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 / N-acetyltransferase domain-containing protein
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsDavies, A.M. / Tata, R. / Chauviac, F.X. / Sutton, B.J. / Brown, P.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of a Putative Acetyltransferase (Pa1377) from Pseudomonas Aeruginosa.
Authors: Davies, A.M. / Tata, R. / Chauviac, F.X. / Sutton, B.J. / Brown, P.R.
History
DepositionNov 28, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / 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
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Jun 12, 2019Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Dec 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ACETYLTRANSFERASE PA1377
B: ACETYLTRANSFERASE PA1377
C: ACETYLTRANSFERASE PA1377
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,49818
Polymers60,2933
Non-polymers1,20515
Water4,774265
1
A: ACETYLTRANSFERASE PA1377
B: ACETYLTRANSFERASE PA1377
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,84810
Polymers40,1962
Non-polymers6528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-70.1 kcal/mol
Surface area15870 Å2
MethodPISA
2
C: ACETYLTRANSFERASE PA1377
hetero molecules

C: ACETYLTRANSFERASE PA1377
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,30016
Polymers40,1962
Non-polymers1,10514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area5020 Å2
ΔGint-62.4 kcal/mol
Surface area15420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.709, 110.928, 134.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-2038-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99935, 0.02185, -0.02857), (0.03554, 0.47843, -0.87741), (-0.0055, -0.87786, -0.47889)-0.8419, 28.29419, 47.83288
2given(-0.99964, -0.02616, -0.00542), (-0.01785, 0.50297, 0.86412), (-0.01988, 0.86391, -0.50325)39.47562, -2.27176, 34.64567

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Components

#1: Protein ACETYLTRANSFERASE PA1377


Mass: 20097.773 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAC1 / Plasmid: PET24A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I3W7
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.48 Å3/Da / Density % sol: 50.4 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: HANGING DROP VAPOR DIFFUSION. RESERVOIR OF 500 MICROLITRES 0.1M TRIS-HCL AT PH6.5, 1.6M AMMONIUM SULFATE AND 0.1% SODIUM AZIDE. DROPS CONTAINED 1 MICROLITRE OF PROTEIN AT 13MG /ML AND AN ...Details: HANGING DROP VAPOR DIFFUSION. RESERVOIR OF 500 MICROLITRES 0.1M TRIS-HCL AT PH6.5, 1.6M AMMONIUM SULFATE AND 0.1% SODIUM AZIDE. DROPS CONTAINED 1 MICROLITRE OF PROTEIN AT 13MG /ML AND AN EQUAL VOLUME OF RESERVOIR. DROPS WERE KEPT AT 291K.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.25→64.3 Å / Num. obs: 28683 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 39.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GE3

2ge3


Resolution: 2.25→64.3 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: MOLECULES A AND B OF THE ASYMMETRIC UNIT FORM THE ASSUMED DIMERIC, BIOLOGICAL UNIT. MOLECULE C FORMS A DIMER WITH A MOLECULE RELATED BY CRYSTALLOGRAPHIC SYMMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1394 4.9 %RANDOM
Rwork0.191 ---
obs0.191 28683 99.9 %-
Solvent computationBsol: 42.52 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.25 Å
Luzzati sigma a0.26 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.25→64.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 72 265 4146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
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_deg1.37
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
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: 2.25→2.33 Å / Num. reflection Rfree: 136 / Num. reflection Rwork: 2684 / Total num. of bins used: 10

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