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- PDB-2dlb: X-ray Crystal Structure of Protein yopT from Bacillus subtilis. N... -

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Basic information

Entry
Database: PDB / ID: 2dlb
TitleX-ray Crystal Structure of Protein yopT from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR412
ComponentsyopT
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / sr412 / NESG / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyProtein of unknown function YopT / Protein of unknown function YopT / YopT domain superfamily / Hypothetical protein Yopt / Ubiquitin-like (UB roll) / Roll / Alpha Beta / SPbeta prophage-derived uncharacterized protein YopT
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.2 Å
AuthorsKuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. ...Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be published
Title: X-ray structure of hypothetical protein from Bacillus subtilis O34498 at the resolution of 1.2A. NESG target SR412
Authors: Kuzin, A.P. / Chen, Y. / Seetharaman, J. / Ho, C.-K. / Cunningham, K. / Janjua, H. / Conover, K. / Ma, L.-C. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: yopT
B: yopT


Theoretical massNumber of molelcules
Total (without water)18,4982
Polymers18,4982
Non-polymers00
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-31 kcal/mol
Surface area8110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.347, 76.116, 78.385
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIn according to Dynamic Light Scattering SR412 is dimer.

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Components

#1: Protein yopT


Mass: 9249.060 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pE21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O34498
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.71 Å3/Da / Density % sol: 52.83 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M lithium sulfate, 0.1M sodium citrate, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9787, 0.9794, 0.9678
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 9, 2006 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97871
20.97941
30.96781
ReflectionResolution: 1.2→30 Å / Num. all: 53757 / Num. obs: 53730 / % possible obs: 87.5 % / Observed criterion σ(I): -3
Reflection shellResolution: 1.2→1.24 Å / % possible all: 59.6

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
ADSCdata collection
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.2→30 Å / Num. parameters: 11721 / Num. restraintsaints: 14189 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: Anisotropic refinement reduced free r (no cutoff) by
RfactorNum. reflection% reflectionSelection details
Rfree0.173 --RANDOM
all0.1543 51040 --
obs-53730 83.1 %-
Refine analyzeNum. disordered residues: 6 / Occupancy sum hydrogen: 1100.5 / Occupancy sum non hydrogen: 1281
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1114 0 0 180 1294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.031
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0305
X-RAY DIFFRACTIONs_zero_chiral_vol0.068
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.073
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.032
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.064
X-RAY DIFFRACTIONs_approx_iso_adps0.093

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