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- PDB-4hzd: Crystal structure of Serine acetyltransferase in complex with Coe... -

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Basic information

Entry
Database: PDB / ID: 4hzd
TitleCrystal structure of Serine acetyltransferase in complex with Coenzyme A from Brucella abortus strain S19
ComponentsCysE, serine acetyltransferase
KeywordsTRANSFERASE / Left handed beta-helical (LBH) domain / Cysteine biosynthesis / serine acetyltransferase
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. ...serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, LbH domain / Serine O-acetyltransferase / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COENZYME A / Serine acetyltransferase / Serine acetyltransferase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.87 Å
AuthorsKumar, S. / Samudrala, G.
CitationJournal: Biochim.Biophys.Acta / Year: 2014
Title: Crystal structure of serine acetyl transferase from Brucella abortus and its complex with coenzyme A.
Authors: Kumar, S. / Kumar, N. / Alam, N. / Gourinath, S.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Aug 13, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CysE, serine acetyltransferase
B: CysE, serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2166
Polymers61,8702
Non-polymers2,3464
Water2,684149
1
A: CysE, serine acetyltransferase
B: CysE, serine acetyltransferase
hetero molecules

A: CysE, serine acetyltransferase
B: CysE, serine acetyltransferase
hetero molecules

A: CysE, serine acetyltransferase
B: CysE, serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,64918
Polymers185,6116
Non-polymers7,03812
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area20120 Å2
ΔGint-144 kcal/mol
Surface area49650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.347, 104.347, 105.675
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-457-

HOH

21A-473-

HOH

31B-451-

HOH

41B-467-

HOH

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Components

#1: Protein CysE, serine acetyltransferase


Mass: 30935.123 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: S19 / Gene: BAbS19_I11940, CysE / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2S6A2, UniProt: A0A0F6AR69*PLUS
#2: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 5% PEG 1000, 5% PEG 3350, 5% MPD, 0.1 M Ethylene glycol, Tris 100 mM, 20-40 mM MgCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5417 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5417 Å / Relative weight: 1
ReflectionResolution: 1.87→100 Å / Num. obs: 35422 / Rmerge(I) obs: 0.1 / Rsym value: 0.0679
Reflection shellResolution: 1.87→1.918 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
AUTOMARdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.87→68.68 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2265 / WRfactor Rwork: 0.1776 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.8568 / SU B: 3.782 / SU ML: 0.111 / SU R Cruickshank DPI: 0.166 / SU Rfree: 0.1541 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2342 1767 5 %RANDOM
Rwork0.1826 ---
obs0.1852 35303 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.13 Å2 / Biso mean: 29.3803 Å2 / Biso min: 12.61 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20.67 Å20 Å2
2--1.33 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 1.87→68.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3788 0 57 149 3994
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193930
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9595349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3175493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38823.099171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7415613
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1181530
X-RAY DIFFRACTIONr_chiral_restr0.1180.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212975
LS refinement shellResolution: 1.87→1.918 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 128 -
Rwork0.291 2304 -
all-2432 -
obs--90.95 %

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