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- PDB-3dl3: Crystal structure of the tellurite resistance protein TehB. North... -

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Basic information

Entry
Database: PDB / ID: 3dl3
TitleCrystal structure of the tellurite resistance protein TehB. Northeast Structural Genomics Consortium target VfR98 .
ComponentsTellurite resistance protein B
Keywordsstructural genomics / unknown function / X-Ray NESG VfR98 Q5E3X2_VIBF1 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyTellurite resistance predicted, YeaR / Domain of unknown function DUF1971 / Domain of unknown function (DUF1971) / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta / Tellurite resistance protein B
Function and homology information
Biological speciesVibrio fischeri ES114 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the tellurite resistance protein TehB. Northeast Structural Genomics Consortium target VfR98.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Wang, D. / Mao, L. / Maglaqui, M. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionJun 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tellurite resistance protein B
B: Tellurite resistance protein B
D: Tellurite resistance protein B
E: Tellurite resistance protein B
G: Tellurite resistance protein B
H: Tellurite resistance protein B
F: Tellurite resistance protein B
I: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)111,6018
Polymers111,6018
Non-polymers00
Water1,51384
1
D: Tellurite resistance protein B

F: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area1900 Å2
ΔGint-17 kcal/mol
Surface area10220 Å2
MethodPISA
2
A: Tellurite resistance protein B

H: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area1720 Å2
ΔGint-17 kcal/mol
Surface area9770 Å2
MethodPISA
3
B: Tellurite resistance protein B
E: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-16 kcal/mol
Surface area10330 Å2
MethodPISA
4
G: Tellurite resistance protein B
I: Tellurite resistance protein B


Theoretical massNumber of molelcules
Total (without water)27,9002
Polymers27,9002
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-15 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.574, 205.020, 56.356
Angle α, β, γ (deg.)90.00, 110.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tellurite resistance protein B


Mass: 13950.108 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri ES114 (bacteria) / Gene: tehB, VF_1779 / References: UniProt: Q5E3X2
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / pH: 6
Details: 0.1M MgCl2 0.1M MES 40% PEG400, pH 6.0, Crystals were grown by microbatch under oil method. temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.979
SYNCHROTRONNSLS X4C2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 17, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 82534 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.072 / Net I/σ(I): 19.6
Reflection shellResolution: 2.27→2.35 Å / Mean I/σ(I) obs: 3.1 / Rsym value: 0.293

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→19.9 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 320301.99 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3617 4.9 %RANDOM
Rwork0.232 ---
obs0.232 74329 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.9961 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 47.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.74 Å20 Å20.78 Å2
2---4.54 Å20 Å2
3---9.28 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6488 0 0 84 6572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 512 4.8 %
Rwork0.274 10102 -
obs--78.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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