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- PDB-3cpk: Crystal structure of the Q7W7N7_BORPA protein from Bordetella par... -

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Basic information

Entry
Database: PDB / ID: 3cpk
TitleCrystal structure of the Q7W7N7_BORPA protein from Bordetella parapertussis. Northeast Structural Genomics Consortium target BeR31
ComponentsUncharacterized protein Q7W7N7_BORPA
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Q7W7N7_BORPA / BPP2477 / BeR31 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyHypothetical Protein Mth938; Chain: A, / MTH938-like / NDUFAF3/Mth938 domain-containing protein / MTH938-like superfamily / Protein of unknown function (DUF498/DUF598) / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesBordetella parapertussis 12822 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsVorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Q7W7N7_BORPA protein from Bordetella parapertussis.
Authors: Vorobiev, S.M. / Abashidze, M. / Seetharaman, J. / Zhao, L. / Janjua, H. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 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 Q7W7N7_BORPA


Theoretical massNumber of molelcules
Total (without water)15,9901
Polymers15,9901
Non-polymers00
Water79344
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.510, 43.510, 118.224
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS A MONOMER ACCORDING TO AGGREGATION SCREENING

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Components

#1: Protein Uncharacterized protein Q7W7N7_BORPA


Mass: 15990.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella parapertussis 12822 (bacteria)
Species: Bordetella parapertussis / Strain: 12822 / NCTC 13253 / Gene: BPP2477 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q7W7N7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 1.75 Å3/Da / Density % sol: 29.7 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15-20% PEG 8000, 0.1M Manganese chloride, 0.1M MOPS pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901, 0.97928, 0.96785
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 30, 2008
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979281
30.967851
ReflectionResolution: 2.5→50 Å / Num. all: 15148 / Num. obs: 15148 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 20.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.95 / Num. unique all: 1546 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→40.83 Å / Rfactor Rfree error: 0.014 / Data cutoff high absF: 372303.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Bijvoet differences were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.253 345 5.4 %RANDOM
Rwork0.209 ---
obs0.209 6408 85.4 %-
all-7502 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.2715 Å2 / ksol: 0.351461 e/Å3
Displacement parametersBiso mean: 44.3 Å2
Baniso -1Baniso -2Baniso -3
1-11.08 Å20 Å20 Å2
2--11.08 Å20 Å2
3----22.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms852 0 0 44 896
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.042 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 44 5.4 %
Rwork0.261 775 -
obs--66 %
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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