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- PDB-4ea9: X-ray structure of GDP-perosamine N-acetyltransferase in complex ... -

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Basic information

Entry
Database: PDB / ID: 4ea9
TitleX-ray structure of GDP-perosamine N-acetyltransferase in complex with transition state analog at 0.9 Angstrom resolution
ComponentsPerosamine N-acetyltransferase
KeywordsTRANSFERASE / beta helix / acetyltransferase / acetyl coenzyme A / GDP-perosamine
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid ...Sialic acid O-acyltransferase NeuD-like / PglD, N-terminal / PglD N-terminal domain / : / Rossmann fold - #20 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
GDP-N-acetylperosamine-coenzyme A / Putative acetyltransferase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsThoden, J.B. / Reinhardt, L.A. / Cook, P.D. / Menden, P. / Cleland, W.W. / Holden, H.M.
CitationJournal: Biochemistry / Year: 2012
Title: Catalytic Mechanism of Perosamine N-Acetyltransferase Revealed by High-Resolution X-ray Crystallographic Studies and Kinetic Analyses.
Authors: Thoden, J.B. / Reinhardt, L.A. / Cook, P.D. / Menden, P. / Cleland, W.W. / Holden, H.M.
History
DepositionMar 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Perosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,3995
Polymers21,9101
Non-polymers1,4884
Water6,161342
1
A: Perosamine N-acetyltransferase
hetero molecules

A: Perosamine N-acetyltransferase
hetero molecules

A: Perosamine N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,19615
Polymers65,7313
Non-polymers4,46512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area4280 Å2
ΔGint-29 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.818, 114.818, 114.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-1264-

HOH

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Components

#1: Protein Perosamine N-acetyltransferase / PerB / Hexapeptide transferase family protein


Mass: 21910.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (bacteria) / Gene: CC_1011, wbqR / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3)
References: UniProt: O85353, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-JBT / GDP-N-acetylperosamine-coenzyme A


Mass: 1381.928 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H64N13O30P5S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 25-30% PEG5000 MME, 100 mM HEPES, pH 7.5, 10 mM CoA, 10 mM GDP-perosamine, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.667 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2009
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.667 Å / Relative weight: 1
ReflectionResolution: 0.9→50 Å / Num. all: 181485 / Num. obs: 181485 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 50.6
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.4 / Num. unique all: 8807 / Rsym value: 0.36 / % possible all: 95.9

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Processing

Software
NameClassification
HKL-3000data collection
PHASERphasing
SHELXL-97refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EA7

4ea7


Resolution: 0.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.155 9076 -RANDOM
Rwork0.138 ---
all0.139 181331 --
obs0.139 181331 98.6 %-
Refinement stepCycle: LAST / Resolution: 0.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1439 0 91 342 1872

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