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- PDB-3fgb: Crystal structure of the Q89ZH8_BACTN protein from Bacteroides th... -

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Basic information

Entry
Database: PDB / ID: 3fgb
TitleCrystal structure of the Q89ZH8_BACTN protein from Bacteroides thetaiotaomicron. Northeast Structural Genomics Consortium target BtR289b.
Componentsuncharacterized protein Q89ZH8_BACTN
Keywordsstructural genomics / unknown function / Q89ZH8_BACTN / BTR289B / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


6-phosphogluconolactonase activity / cytosol
Similarity search - Function
Lactonase, 7-bladed beta propeller / Lactonase, 7-bladed beta-propeller / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsVorobiev, S.M. / Lew, S. / Seetharaman, J. / Lee, D. / Foote, L.E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. ...Vorobiev, S.M. / Lew, S. / Seetharaman, J. / Lee, D. / Foote, L.E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q89ZH8_BACTN protein from Bacteroides thetaiotaomicron.
Authors: Vorobiev, S.M. / Lew, S. / Seetharaman, J. / Lee, D. / Foote, L.E. / Ciccosanti, C. / Janjua, H. / Xiao, R. / Acton, T. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionDec 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein Q89ZH8_BACTN
B: uncharacterized protein Q89ZH8_BACTN


Theoretical massNumber of molelcules
Total (without water)79,1792
Polymers79,1792
Non-polymers00
Water11,944663
1
A: uncharacterized protein Q89ZH8_BACTN


Theoretical massNumber of molelcules
Total (without water)39,5901
Polymers39,5901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: uncharacterized protein Q89ZH8_BACTN


Theoretical massNumber of molelcules
Total (without water)39,5901
Polymers39,5901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.478, 85.082, 99.429
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer according to aggregation screening

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Components

#1: Protein uncharacterized protein Q89ZH8_BACTN


Mass: 39589.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148/DSM 2079/NCTC 10582/E50/VPI-5482 / Gene: BT_4399 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q89ZH8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 663 / 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: 42.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20% PEG 20000, 0.035M potassium chloride, 0.1M Tris.HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97941, 0.97960, 0.96862
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 21, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.97961
30.968621
ReflectionResolution: 2→50 Å / Num. all: 94601 / Num. obs: 94128 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Biso Wilson estimate: 4.5 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 18.6
Reflection shellResolution: 2→2.14 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 7.3 / Num. unique all: 10495 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDEphasing
RESOLVEmodel building
CNS1.2refinement
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→42.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 198428.07 / 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
Rfree0.24 2791 4 %RANDOM
Rwork0.225 ---
obs0.225 70656 80.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.2651 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 20.6 Å2
Baniso -1Baniso -2Baniso -3
1-17.07 Å20 Å20 Å2
2---8.36 Å20 Å2
3----8.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→42.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5294 0 0 663 5957
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
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: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.239 347 3.5 %
Rwork0.239 9445 -
obs--66.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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