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- PDB-1zn6: X-ray Crystal Structure of Protein Q7WLM8 from Bordetella bronchi... -

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Basic information

Entry
Database: PDB / ID: 1zn6
TitleX-ray Crystal Structure of Protein Q7WLM8 from Bordetella bronchiseptica. Northeast Structural Genomics Consortium Target BoR19.
Componentsphage-related conserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / novel / BoR19 / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


: / Hydrolases; Acting on peptide bonds (peptidases) / single-stranded DNA binding / peptidase activity / DNA damage response
Similarity search - Function
SOS response associated peptidase-like / hypothetical protein yedk fold / SOS response associated peptidase (SRAP) / SOS response associated peptidase-like / SOS response associated peptidase (SRAP) / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Abasic site processing protein / Abasic site processing protein
Similarity search - Component
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKuzin, A.P. / Yong, W. / Vorobiev, S.M. / Xiao, R. / Ma, L.-C. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Novel structure of the hypothetical protein Q7WLM8 from Bordetella bronchiseptica. Northeast Structural Genomics Consortium target BoR19.
Authors: Kuzin, A.P. / Yong, W. / Vorobiev, S.M. / Xiao, R. / Ma, L.-C. / Acton, T. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionMay 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phage-related conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4914
Polymers26,2021
Non-polymers2883
Water3,603200
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.406, 87.210, 64.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein phage-related conserved hypothetical protein


Mass: 26202.381 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Strain: RB50 / Gene: BB1717 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) + Magic / References: UniProt: Q7WLM8, UniProt: A0A0H3LKE5*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4M Ammonium sulfate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97922 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 6, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 42139 / Num. obs: 41842 / % possible obs: 98.4 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 11.9 Å2
Reflection shellResolution: 1.8→1.86 Å / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→28.43 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 238589.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 1987 4.9 %RANDOM
Rwork0.2033 ---
obs0.2033 40377 94.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.224 Å2 / ksol: 0.369242 e/Å3
Displacement parametersBiso mean: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.413 Å20 Å20 Å2
2---1.524 Å20 Å2
3---0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.8→28.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1684 0 15 200 1899
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 317 5 %
Rwork0.214 6041 -
obs--89.6 %
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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