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- PDB-3i1i: X-ray crystal structure of homoserine O-acetyltransferase from Ba... -

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Basic information

Entry
Database: PDB / ID: 3i1i
TitleX-ray crystal structure of homoserine O-acetyltransferase from Bacillus anthracis
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / structural genomics / IDP01610 / homoserine / O-acetyltransferase / Bacillus anthracis / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


homoserine metabolic process / homoserine O-acetyltransferase activity / methionine biosynthetic process / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cytoplasm
Similarity search - Function
Homoserine/serine acetyltransferase MetX-like / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / PHOSPHATE ION / Probable acyltransferase / Probable acyltransferase
Similarity search - Component
Biological speciesBacillus anthracis str. 'Ames Ancestor' (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.44 Å
AuthorsOsipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be published
Title: X-ray crystal structure of homoserine O-acetyltransferase from Bacillus anthracis.
Authors: Osipiuk, J. / Zhou, M. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A.
History
DepositionJun 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)87,7816
Polymers87,4402
Non-polymers3414
Water6,251347
1
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules

A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,56312
Polymers174,8814
Non-polymers6828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area5690 Å2
ΔGint-25.9 kcal/mol
Surface area28120 Å2
MethodPISA
2
A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules

A: Homoserine O-acetyltransferase
B: Homoserine O-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,56312
Polymers174,8814
Non-polymers6828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area5660 Å2
ΔGint-26.9 kcal/mol
Surface area28360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.221, 123.221, 295.169
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsAUTHORS STATE THAT THE ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE.

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Components

#1: Protein Homoserine O-acetyltransferase


Mass: 43720.152 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. 'Ames Ancestor' (bacteria)
Strain: Ames Ancestor, A2084 / Gene: BAS4629, BA_4983, GBAA4983, GBAA_4983 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81KL4, UniProt: A0A6L7HCR9*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.7 Å3/Da / Density % sol: 66.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris buffer, 1 M Ammonium phosphate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2009
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.44→47.3 Å / Num. all: 50355 / Num. obs: 50355 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.3 % / Biso Wilson estimate: 49.4 Å2 / Rmerge(I) obs: 0.134 / Χ2: 2.425 / Net I/σ(I): 28.003
Reflection shellResolution: 2.44→2.48 Å / Redundancy: 8 % / Rmerge(I) obs: 0.791 / Mean I/σ(I) obs: 2.81 / Num. unique all: 2470 / Χ2: 0.988 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.005data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.44→47.3 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 10.128 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.218 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2539 5.1 %RANDOM
Rwork0.161 ---
all0.163 50039 --
obs0.163 50039 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.1 Å2 / Biso mean: 28.708 Å2 / Biso min: 4.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.62 Å20 Å2
2--1.25 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 2.44→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5961 0 20 347 6328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0226237
X-RAY DIFFRACTIONr_bond_other_d0.0010.024214
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9478461
X-RAY DIFFRACTIONr_angle_other_deg0.926310318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8565775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89924.718301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.98151105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3881527
X-RAY DIFFRACTIONr_chiral_restr0.0890.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216937
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021244
X-RAY DIFFRACTIONr_mcbond_it0.7411.53760
X-RAY DIFFRACTIONr_mcbond_other0.1661.51518
X-RAY DIFFRACTIONr_mcangle_it1.45626104
X-RAY DIFFRACTIONr_scbond_it2.68332477
X-RAY DIFFRACTIONr_scangle_it4.0984.52341
LS refinement shellResolution: 2.44→2.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 172 -
Rwork0.219 3385 -
all-3557 -
obs-3557 97.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0958-0.0452-0.31360.18420.06881.1417-0.02480.0013-0.01260.01620.0074-0.02280.0788-0.03770.01740.08030.00890.00120.01290.01240.02461.2295104.346919.0727
20.21680.2051-0.05910.3380.06780.8899-0.0240.07160.0339-0.0480.05030.0578-0.0508-0.2223-0.02640.02390.00930.01150.07370.02410.0332-15.168692.320562.3995
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 373
2X-RAY DIFFRACTION2B1 - 372

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