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- PDB-1sst: Serine Acetyltransferase- Complex with CoA -

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Basic information

Entry
Database: PDB / ID: 1sst
TitleSerine Acetyltransferase- Complex with CoA
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / LEFT-HANDED PARALLEL BETA HELIX
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity / cysteine biosynthetic process from serine / cytosol
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
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOlsen, L.R. / Huang, B. / Vetting, M.W. / Roderick, S.L.
CitationJournal: Biochemistry / Year: 2004
Title: Structure of Serine Acetyltransferase in Complexes with CoA and its Cysteine Feedback Inhibitor
Authors: Olsen, L.R. / Huang, B. / Vetting, M.W. / Roderick, S.L.
History
DepositionMar 24, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,8986
Polymers87,5953
Non-polymers2,3033
Water3,099172
1
A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules

A: Serine acetyltransferase
B: Serine acetyltransferase
C: Serine acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,79612
Polymers175,1906
Non-polymers4,6056
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area24900 Å2
ΔGint-102 kcal/mol
Surface area43680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)111.300, 125.000, 103.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is hexameric. The deposited coordinates correspond to a trimer. A crystallographic twofold rotation parallel to the y-axis and passing through the point x=1/2, z=1/4 creates the biological unit.

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Components

#1: Protein Serine acetyltransferase / SAT


Mass: 29198.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: CYSE, HI0606 / Plasmid: pET3a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P43886, serine O-acetyltransferase
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.04 Å3/Da / Density % sol: 39.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% (v/v) polyethylene glycol 400, 130 mM LiCl, 50 mM CoA, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 25, 2003 / Details: Osmic Blue
RadiationMonochromator: Osmic Blue / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→31.25 Å / Num. all: 44011 / Num. obs: 44011 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.029
Reflection shellResolution: 2→2.13 Å / Rmerge(I) obs: 0.153 / % possible all: 88.8

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1ssm

1ssm


Resolution: 2→31.25 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1088857.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2215 5 %RANDOM
Rwork0.223 ---
obs0.225 44011 90.2 %-
all-44011 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4397 Å2 / ksol: 0.370295 e/Å3
Displacement parametersBiso mean: 35.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.73 Å20 Å20 Å2
2--4.43 Å20 Å2
3---1.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2→31.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5390 0 144 172 5706
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d1.11
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 367 5.1 %
Rwork0.259 6760 -
obs-6760 88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4COA.PARCOA.TOP

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