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- PDB-1t82: Crystal Structure of the putative thioesterase from Shewanella on... -

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Basic information

Entry
Database: PDB / ID: 1t82
TitleCrystal Structure of the putative thioesterase from Shewanella oneidensis, Northeast Structural Genomics Target SoR51
Componentshypothetical acetyltransferase
KeywordsTRANSFERASE / structural genomics / alpha-beta dimeric protein with a fold resembling a hotdog / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyThioesterase, putative / Putative thioesterase (yiiD_Cterm) / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / acyltransferase activity, transferring groups other than amino-acyl groups / Roll / Alpha Beta / Thioesterase domain protein YiiD
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsForouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the putative thioesterase from Shewanella oneidensis, Northeast Structural Genomics Target SoR51
Authors: Forouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical acetyltransferase
B: hypothetical acetyltransferase
C: hypothetical acetyltransferase
D: hypothetical acetyltransferase


Theoretical massNumber of molelcules
Total (without water)71,4064
Polymers71,4064
Non-polymers00
Water7,819434
1
A: hypothetical acetyltransferase
B: hypothetical acetyltransferase


Theoretical massNumber of molelcules
Total (without water)35,7032
Polymers35,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-19 kcal/mol
Surface area13060 Å2
MethodPISA
2
C: hypothetical acetyltransferase
D: hypothetical acetyltransferase


Theoretical massNumber of molelcules
Total (without water)35,7032
Polymers35,7032
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2390 Å2
ΔGint-23 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.980, 49.669, 99.670
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical acetyltransferase


Mass: 17851.510 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Strain: MR-1 / Plasmid: BL21(DE3)+Magic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8E989
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / 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: 2.1 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10mM Tris, 100mM NaCl, 5mM DTT. Reservoir solution: 20% PEG 3350, 200mM sodium formate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→29.81 Å / Num. all: 112723 / Num. obs: 107847 / % possible obs: 92.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.43 % / Biso Wilson estimate: 12.4 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.079 / Net I/σ(I): 21
Reflection shellResolution: 1.7→1.81 Å / Redundancy: 4 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 9.73 / Num. unique all: 15130 / Rsym value: 0.171 / % possible all: 86.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBthen SOLVEphasing
CNSrefinement
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.81 Å
Isotropic thermal model: anisotropic and overall temperature factors
Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 10507 -random
Rwork0.194 ---
all-107847 --
obs-107847 92.9 %-
Displacement parametersBiso mean: 15.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.7 Å20 Å2-2.47 Å2
2--1.64 Å20 Å2
3----0.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4497 0 0 434 4931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.005
RfactorNum. reflection% reflection
Rfree0.221 10507 -
Rwork0.189 --
obs-15130 10.1 %

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