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- PDB-3vvm: Crystal structure of G52A-P55G mutant of L-serine-O-acetyltransfe... -

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Basic information

Entry
Database: PDB / ID: 3vvm
TitleCrystal structure of G52A-P55G mutant of L-serine-O-acetyltransferase found in D-cycloserine biosynthetic pathway
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / D-cycloserine / alpha/beta hydrolase domain / L-serine-O-acetyltransferase
Function / homology
Function and homology information


O-succinyltransferase activity / homoserine O-acetyltransferase / homoserine O-acetyltransferase activity / serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
Rna Polymerase Sigma Factor; Chain: A - #110 / Homoserine/serine acetyltransferase MetX-like / Rna Polymerase Sigma Factor; Chain: A / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Rna Polymerase Sigma Factor; Chain: A - #110 / Homoserine/serine acetyltransferase MetX-like / Rna Polymerase Sigma Factor; Chain: A / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
L-serine/homoserine O-acetyltransferase
Similarity search - Component
Biological speciesStreptomyces lavendulae subsp. lavendulae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOda, K. / Matoba, Y. / Kumagai, T. / Noda, M. / Sugiyama, M.
CitationJournal: J.Bacteriol. / Year: 2013
Title: Crystallographic study to determine the substrate specificity of an L-serine-acetylating enzyme found in the D-cycloserine biosynthetic pathway
Authors: Oda, K. / Matoba, Y. / Kumagai, T. / Noda, M. / Sugiyama, M.
History
DepositionJul 26, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)84,9222
Polymers84,9222
Non-polymers00
Water7,458414
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-21 kcal/mol
Surface area27110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.560, 102.330, 147.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Homoserine O-acetyltransferase / / Homoserine O-trans-acetylase


Mass: 42460.785 Da / Num. of mol.: 2 / Mutation: G52A, P55G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lavendulae subsp. lavendulae (bacteria)
Strain: ATCC11924 / Gene: dcsE, metX / Plasmid: pET-28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: D2Z028, homoserine O-acetyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 414 / 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: 2.07 Å3/Da / Density % sol: 40.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG4000, Tris, ammonium acetate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2010
RadiationMonochromator: Fixed exit double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 78450 / Num. obs: 78450 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 38.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 5.4 / Num. unique all: 7725 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B61

2b61


Resolution: 1.7→24 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2345468.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.214 3893 5 %RANDOM
Rwork0.192 ---
obs0.192 77226 98.5 %-
all-77226 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6321 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.03 Å20 Å20 Å2
2--1.52 Å20 Å2
3----6.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5574 0 0 414 5988
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.181.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.832.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 645 5.1 %
Rwork0.218 11891 -
obs--97.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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