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- PDB-3jvn: Crystal Structure of the acetyltransferase VF_1542 from Vibrio fi... -

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Basic information

Entry
Database: PDB / ID: 3jvn
TitleCrystal Structure of the acetyltransferase VF_1542 from Vibrio fischeri, Northeast Structural Genomics Consortium Target VfR136
ComponentsAcetyltransferase
KeywordsTRANSFERASE / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / Acyltransferase
Function / homology
Function and homology information


N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Similarity search - Function
Acetyltransferase (GNAT) family / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.61 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target VfR136
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Zhao, L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Aug 7, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3112
Polymers20,2151
Non-polymers961
Water48627
1
A: Acetyltransferase
hetero molecules

A: Acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6224
Polymers40,4302
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area1790 Å2
ΔGint-41 kcal/mol
Surface area15240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.714, 105.332, 73.872
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Acetyltransferase


Mass: 20214.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (bacteria) / Strain: ES114 / Gene: VF_1542 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic
References: UniProt: Q5E4K9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 277 K / Method: microbatch, under oil / pH: 5.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5). Reservoir solution: 0.1M Bis Tris (pH 5.5), 1% PEG 3350, and 0.1M ammonium sulfate, microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 3, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 10548 / Num. obs: 8101 / % possible obs: 76.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 31.6 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.054 / Net I/σ(I): 24.93
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.082 / Mean I/σ(I) obs: 7.97 / Num. unique all: 1051 / Rsym value: 0.101 / % possible all: 52.3

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBthen SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.61→19.13 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 318924.312 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 417 5.2 %RANDOM
Rwork0.233 ---
all0.335 10531 --
obs0.334 8088 76.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.501 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 40.1 Å2
Baniso -1Baniso -2Baniso -3
1--5.63 Å20 Å20 Å2
2--14.5 Å20 Å2
3----8.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.61→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 5 27 1034
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.7
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.07 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 26 5.1 %
Rwork0.3 482 -
obs-508 48.4 %

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