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- PDB-3bhp: Crystal structure of UPF0291 protein ynzC from Bacillus subtilis ... -

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Basic information

Entry
Database: PDB / ID: 3bhp
TitleCrystal structure of UPF0291 protein ynzC from Bacillus subtilis at resolution 2.0 A. Northeast Structural Genomics Consortium target SR384
ComponentsUPF0291 protein ynzC
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NESG / SR384 / O31818 / UPF0291 protein ynzC / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Cytoplasm
Function / homologyProtein of unknown function DUF896 / Bacterial protein of unknown function (DUF896) / Helix hairpin bin / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / cytoplasm / UPF0291 protein YnzC
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.01 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Janjua, H. / Cunningham, K. / Maglaqui, M. / Owens, L.A. / Zhao, L. / Xiao, R. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Janjua, H. / Cunningham, K. / Maglaqui, M. / Owens, L.A. / Zhao, L. / Xiao, R. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the UPF0291 protein ynzC from Bacillus subtilis at the resolution 2.0 A.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Janjua, H. / Cunningham, K. / Maglaqui, M. / Owens, L.A. / Zhao, L. / Xiao, R. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionNov 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UPF0291 protein ynzC
B: UPF0291 protein ynzC
C: UPF0291 protein ynzC


Theoretical massNumber of molelcules
Total (without water)21,0833
Polymers21,0833
Non-polymers00
Water3,531196
1
A: UPF0291 protein ynzC


Theoretical massNumber of molelcules
Total (without water)7,0281
Polymers7,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: UPF0291 protein ynzC


Theoretical massNumber of molelcules
Total (without water)7,0281
Polymers7,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: UPF0291 protein ynzC


Theoretical massNumber of molelcules
Total (without water)7,0281
Polymers7,0281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.279, 38.460, 86.785
Angle α, β, γ (deg.)90.00, 107.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-117-

HOH

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Components

#1: Protein UPF0291 protein ynzC


Mass: 7027.784 Da / Num. of mol.: 3 / Fragment: Residues 1-52
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: ynzC, BSU17880 / Production host: Escherichia coli (E. coli) / References: UniProt: O31818
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M KH2PO4, 0.1M Na Citrate, 40% PEG 1000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 9, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 26190 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 15.5 % / Biso Wilson estimate: 7.1 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.4
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.123 / Mean I/σ(I) obs: 10.7 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.01→19.55 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 660559.39 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used in phasing. BULK SOLVENT MODEL USED IN REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 2246 9.3 %RANDOM
Rwork0.2289 ---
obs0.2289 26053 90.7 %-
all-26190 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.6638 Å2 / ksol: 0.45 e/Å3
Displacement parametersBiso mean: 25.9 Å2
Baniso -1Baniso -2Baniso -3
1--5.991 Å20 Å22.001 Å2
2--0.7 Å20 Å2
3---5.291 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a--0.14 Å
Refinement stepCycle: LAST / Resolution: 2.01→19.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1211 0 0 196 1407
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004672
X-RAY DIFFRACTIONc_angle_deg0.82237
X-RAY DIFFRACTIONc_dihedral_angle_d16.3
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.5191.5
X-RAY DIFFRACTIONc_mcangle_it2.3322
X-RAY DIFFRACTIONc_scbond_it2.5552
X-RAY DIFFRACTIONc_scangle_it3.9152.5
LS refinement shellResolution: 2.01→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.21 312 9.8 %
Rwork0.175 2864 -
obs--70.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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