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- PDB-2fe7: The crystal structure of a probable N-acetyltransferase from Pseu... -

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Basic information

Entry
Database: PDB / ID: 2fe7
TitleThe crystal structure of a probable N-acetyltransferase from Pseudomonas aeruginosa
Componentsprobable N-acetyltransferase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / N-acetyltransferase / Pseudomonas aeruginosa / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


N-acetyltransferase activity
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
: / Probable N-acetyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa UCBPP-PA14 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsZhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a N-acetyltransferase from Pseudomonas aeruginosa
Authors: Zhang, R. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionDec 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: probable N-acetyltransferase
B: probable N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)38,2072
Polymers38,2072
Non-polymers00
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-43 kcal/mol
Surface area16120 Å2
MethodPISA
2
A: probable N-acetyltransferase
B: probable N-acetyltransferase

A: probable N-acetyltransferase
B: probable N-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)76,4144
Polymers76,4144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area15520 Å2
ΔGint-96 kcal/mol
Surface area29790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.375, 52.036, 58.970
Angle α, β, γ (deg.)90.00, 94.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-297-

HOH

DetailsThis protein existed as dimer. The deposited structure of MolA and MolB reprsent the dimer in the asymmetric unit.

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Components

#1: Protein probable N-acetyltransferase


Mass: 19103.570 Da / Num. of mol.: 2 / Mutation: Y68F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa UCBPP-PA14 (bacteria)
Species: Pseudomonas aeruginosa / Strain: PAO1 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 32043669, UniProt: Q9I640*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.83 Å3/Da / Density % sol: 56.54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris, 0.02M CaCl2, 20% PEG3350, 3% 1,6 Hexandiol, 3.3% sucrose, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 5, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2→70.53 Å / Num. all: 27833 / Num. obs: 27694 / % possible obs: 99.51 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 17.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.357 / Mean I/σ(I) obs: 2.32 / Num. unique all: 2840 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2→70.53 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.936 / SU B: 6.314 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.146
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22124 1483 5.1 %RANDOM
Rwork0.18753 ---
obs0.18924 27694 99.51 %-
all-27833 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å2-0.41 Å2
2---0.46 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.035 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.036 Å
Refinement stepCycle: LAST / Resolution: 2→70.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2597 0 0 301 2898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222657
X-RAY DIFFRACTIONr_angle_refined_deg1.1721.963602
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125317
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8822.042142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69815429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4811536
X-RAY DIFFRACTIONr_chiral_restr0.0830.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022091
X-RAY DIFFRACTIONr_nbd_refined0.2040.21250
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21830
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2312
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.215
X-RAY DIFFRACTIONr_mcbond_it0.5911.51650
X-RAY DIFFRACTIONr_mcangle_it0.99522533
X-RAY DIFFRACTIONr_scbond_it1.65631198
X-RAY DIFFRACTIONr_scangle_it2.6484.51069
LS refinement shellResolution: 1.996→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 108 -
Rwork0.223 1936 -
obs--95.38 %
Refinement TLS params.Method: refined / Origin x: 28.95 Å / Origin y: 43.715 Å / Origin z: 12.439 Å
111213212223313233
T-0.0245 Å20.0039 Å20.006 Å2--0.0649 Å2-0.003 Å2---0.0719 Å2
L1.1542 °20.3036 °20.0972 °2-1.0057 °20.0404 °2--0.948 °2
S-0.0011 Å °-0.1321 Å °0.0146 Å °0.1036 Å °-0.0047 Å °0.0323 Å °0.0235 Å °-0.0629 Å °0.0058 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 5011 - 58
2X-RAY DIFFRACTION1AA51 - 10059 - 108
3X-RAY DIFFRACTION1AA101 - 158109 - 166
4X-RAY DIFFRACTION1BB-7 - 501 - 58
5X-RAY DIFFRACTION1BB51 - 10059 - 108
6X-RAY DIFFRACTION1BB101 - 158109 - 166

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