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- PDB-3nxh: Crystal Structure of the transcriptional regulator yvhJ from Baci... -

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Basic information

Entry
Database: PDB / ID: 3nxh
TitleCrystal Structure of the transcriptional regulator yvhJ from Bacillus subtilis. Northeast Structural Genomics Consortium Target SR735.
Componentstranscriptional regulator yvhJ
Keywordstranscription regulator / NESG / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Transferases for other substituted phosphate groups / cell wall organization / transferase activity / plasma membrane
Similarity search - Function
LCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Polyisoprenyl-teichoic acid--peptidoglycan teichoic acid transferase TagV
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.584 Å
AuthorsVorobiev, S. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / 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 transcriptional regulator yvhJ from Bacillus subtilis.
Authors: Vorobiev, S. / Chen, Y. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJul 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: transcriptional regulator yvhJ


Theoretical massNumber of molelcules
Total (without water)30,8761
Polymers30,8761
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.136, 67.800, 85.846
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsmonomer,34.36 kD,93.3%

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Components

#1: Protein transcriptional regulator yvhJ


Mass: 30875.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU35520, yvhJ / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P96499
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil
Details: 20% PEG 1000, 0.1M ammonium chloride, 0.1M sodium acetate, Microbatch under Paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97903 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 9, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97903 Å / Relative weight: 1
ReflectionResolution: 2.584→50 Å / Num. all: 15095 / Num. obs: 14808 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 42.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 6.9 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 2.584→36.266 Å / Occupancy max: 1 / Occupancy min: 0.56 / SU ML: 0.45 / σ(F): 1.35 / Phase error: 30.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2963 687 4.65 %
Rwork0.2446 --
obs0.247 14767 96.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.22 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.584→36.266 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1620 0 0 6 1626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111639
X-RAY DIFFRACTIONf_angle_d1.4122218
X-RAY DIFFRACTIONf_dihedral_angle_d19.466577
X-RAY DIFFRACTIONf_chiral_restr0.081263
X-RAY DIFFRACTIONf_plane_restr0.005289
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.584-2.78340.38531150.33622745X-RAY DIFFRACTION94
2.7834-3.06340.34381390.27692915X-RAY DIFFRACTION100
3.0634-3.50640.32611350.25732898X-RAY DIFFRACTION100
3.5064-4.41650.26961670.2122878X-RAY DIFFRACTION100
4.4165-36.26980.26811310.22992644X-RAY DIFFRACTION91
Refinement TLS params.Method: refined / Origin x: 33.2222 Å / Origin y: 21.8867 Å / Origin z: 58.6166 Å
111213212223313233
T0.1809 Å2-0.0028 Å2-0.0238 Å2-0.2225 Å2-0.0002 Å2--0.1921 Å2
L1.7231 °2-0.4409 °2-0.4709 °2-1.1884 °20.372 °2--1.6717 °2
S-0.1319 Å °-0.2961 Å °0.0914 Å °0.0002 Å °0.0044 Å °-0.0004 Å °0.0983 Å °0.2506 Å °0.1123 Å °
Refinement TLS groupSelection details: chain A

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