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- PDB-3f1x: Three dimensional structure of the serine acetyltransferase from ... -

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Basic information

Entry
Database: PDB / ID: 3f1x
TitleThree dimensional structure of the serine acetyltransferase from Bacteroides vulgatus, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BVR62.
ComponentsSerine acetyltransferase
KeywordsTRANSFERASE / NESG X-Ray BvR62 A6KZB9 A6KZB9_BACV8 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


serine O-acetyltransferase / serine O-acetyltransferase activity
Similarity search - Function
serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, N-terminal domain superfamily / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Orthogonal Bundle ...serine acetyltransferase, domain 1 / serine acetyltransferase, domain 1 / Serine acetyltransferase, N-terminal domain superfamily / 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
Serine O-acetyltransferase
Similarity search - Component
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsKuzin, A.P. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Wang, D. / Mao, L. / Cunningham, K. / Maglaqui, M. / Xiao, R. / Liu, J. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Wang, D. / Mao, L. / Cunningham, K. / Maglaqui, M. / Xiao, R. / Liu, J. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Three dimensional structure of the serine acetyltransferase from Bacteroides vulgatus, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BVR62.
Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Wang, D. / Mao, L. / Cunningham, K. / Maglaqui, M. / Xiao, R. / Liu, J. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionOct 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine acetyltransferase


Theoretical massNumber of molelcules
Total (without water)33,9971
Polymers33,9971
Non-polymers00
Water2,756153
1
A: Serine acetyltransferase
x 6


Theoretical massNumber of molelcules
Total (without water)203,9836
Polymers203,9836
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation10_456y-1/3,x+1/3,-z+4/31
crystal symmetry operation11_566x-y+2/3,-y+4/3,-z+4/31
crystal symmetry operation12_556-x+2/3,-x+y+1/3,-z+4/31
Buried area32170 Å2
ΔGint-180 kcal/mol
Surface area61110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.417, 111.417, 124.426
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

#1: Protein Serine acetyltransferase


Mass: 33997.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Gene: BVU_1092 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: A6KZB9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.19 Å3/Da / Density % sol: 43.73 %
Crystal growTemperature: 277 K / pH: 4.2
Details: 0.88M Potassium nitrate, 0.1M Sodium citrate, pH 4.2, microbatch method, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97913, 0.96863, 0.97927
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2008 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979131
20.968631
30.979271
ReflectionResolution: 2→50 Å / Num. obs: 38687 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 24.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 9.4 / Num. unique all: 3422 / % possible all: 86.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SnBphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2→19.44 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 112214.6 / 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
Rfree0.258 1867 5.1 %RANDOM
Rwork0.214 ---
obs0.214 36633 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.8402 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 28.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→19.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2115 0 0 153 2268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 308 5.8 %
Rwork0.23 5046 -
obs--82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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