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- PDB-5jbr: Crystal structure of uncharacterized protein Bcav_2135 from Beute... -

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Basic information

Entry
Database: PDB / ID: 5jbr
TitleCrystal structure of uncharacterized protein Bcav_2135 from Beutenbergia cavernae
ComponentsUncharacterized protein Bcav_2135
KeywordsStructural Genomics / Unknown function / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology: / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / DNA binding / Orthogonal Bundle / Mainly Alpha / Transcriptional regulator
Function and homology information
Biological speciesBeutenbergia cavernae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 Å
AuthorsChang, C. / Cuff, M. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To Be Published
Title: Crystal structure of uncharacterized protein Bcav_2135 from Beutenbergia cavernae
Authors: Chang, C. / Cuff, M. / Hatzos-Skintges, C. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein Bcav_2135
B: Uncharacterized protein Bcav_2135
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2326
Polymers32,8482
Non-polymers3844
Water4,270237
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4580 Å2
ΔGint-76 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.096, 46.461, 47.820
Angle α, β, γ (deg.)104.040, 102.340, 117.670
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized protein Bcav_2135


Mass: 16423.896 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: mutate M1V, A24T / Source: (gene. exp.) Beutenbergia cavernae (bacteria) / Strain: ATCC BAA-8 / DSM 12333 / NBRC 16432 / Gene: Bcav_2135 / Plasmid: pMCSG73
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C5C6I1
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 237 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: Lithium sulfate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9793149 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 17, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793149 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 36092 / % possible obs: 97.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 14.16 Å2 / Rmerge(I) obs: 0.041 / Net I/av σ(I): 29.24 / Net I/σ(I): 11.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.65-1.683.20.517195.3
1.68-1.713.40.47195.7
1.71-1.743.70.444196.1
1.74-1.7840.38195.9
1.78-1.823.90.315196.5
1.82-1.863.90.258196.2
1.86-1.93.90.203196.8
1.9-1.963.90.167196.9
1.96-2.013.90.125196.9
2.01-2.083.90.103197.2
2.08-2.153.90.079197.3
2.15-2.243.90.063197.5
2.24-2.343.90.056197.7
2.34-2.463.90.048197.9
2.46-2.623.90.04198.3
2.62-2.823.90.035198.2
2.82-3.113.90.029198.7
3.11-3.553.90.023198.8
3.55-4.483.90.019199
4.48-503.80.028197.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXdev_2328refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.65→35.433 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 21.28
RfactorNum. reflection% reflection
Rfree0.1994 1589 5.26 %
Rwork0.153 --
obs0.1554 30192 81.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.86 Å2 / Biso mean: 21.6258 Å2 / Biso min: 6.04 Å2
Refinement stepCycle: final / Resolution: 1.65→35.433 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 20 237 2469
Biso mean--63.4 29.66 -
Num. residues----291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062366
X-RAY DIFFRACTIONf_angle_d0.713223
X-RAY DIFFRACTIONf_chiral_restr0.041362
X-RAY DIFFRACTIONf_plane_restr0.004430
X-RAY DIFFRACTIONf_dihedral_angle_d17.1651417
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.70320.3194610.23941157121836
1.7032-1.76410.2902980.20551683178153
1.7641-1.83470.25411200.17722029214964
1.8347-1.91820.21561230.15952339246273
1.9182-2.01940.18711350.14792686282183
2.0194-2.14590.19562030.13683002320594
2.1459-2.31150.19761550.12883127328298
2.3115-2.54410.17421810.13883118329998
2.5441-2.91210.20322100.15163129333998
2.9121-3.66830.18491860.1533140332699
3.6683-35.44090.19921170.16313193331098

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