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- PDB-2b61: Crystal Structure of Homoserine Transacetylase -

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Basic information

Entry
Database: PDB / ID: 2b61
TitleCrystal Structure of Homoserine Transacetylase
ComponentsHomoserine O-acetyltransferase
KeywordsTRANSFERASE / acyl-enzyme / aspartate pathway / coenzyme A / structure-function studies / alpha-beta hydrolase fold
Function / homology
Function and homology information


homoserine metabolic process / homoserine O-acetyltransferase / homoserine O-acetyltransferase activity / methionine biosynthetic process / 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
Homoserine O-acetyltransferase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsMirza, I.A. / Nazi, I. / Korczynska, M. / Wright, G.D. / Berghuis, A.M.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of Homoserine Transacetylase from Haemophilus influenzae Reveals a New Family of alpha/beta-Hydrolases
Authors: Mirza, I.A. / Nazi, I. / Korczynska, M. / Wright, G.D. / Berghuis, A.M.
History
DepositionSep 29, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Nov 13, 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
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
Remark 999SEQUENCE The sequence is obtained from wild type H.influenzae 49824 and the conflicts are due to ...SEQUENCE The sequence is obtained from wild type H.influenzae 49824 and the conflicts are due to different strain.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homoserine O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)42,5391
Polymers42,5391
Non-polymers00
Water7,656425
1
A: Homoserine O-acetyltransferase

A: Homoserine O-acetyltransferase


Theoretical massNumber of molelcules
Total (without water)85,0792
Polymers85,0792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area4570 Å2
ΔGint-23 kcal/mol
Surface area25980 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)85.264, 85.264, 120.263
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-732-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -X, -X+Y, -Z+1/3

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Components

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


Mass: 42539.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: metX, met2 / Plasmid: pET28+hom2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P45131, homoserine O-acetyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.9 Å3/Da / Density % sol: 56.2 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: PEG8000, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 60657 / Num. obs: 57586 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellHighest resolution: 1.65 Å / % possible all: 98.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.7data extraction
CBASSdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.243 / SU ML: 0.044 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.075 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3071 5.1 %RANDOM
Rwork0.163 ---
all0.165 60657 --
obs0.164 57586 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.706 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20.19 Å20 Å2
2--0.38 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2823 0 0 425 3248
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222921
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9493965
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4825364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28924.621145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24415468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.181512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2417
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022293
X-RAY DIFFRACTIONr_nbd_refined0.1910.21387
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2327
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.229
X-RAY DIFFRACTIONr_mcbond_it0.8411.51837
X-RAY DIFFRACTIONr_mcangle_it1.24722866
X-RAY DIFFRACTIONr_scbond_it2.03831251
X-RAY DIFFRACTIONr_scangle_it2.9264.51099
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 243 -
Rwork0.198 4195 -
all-4438 -
obs--98.51 %

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