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- PDB-3lyw: Crystal structure of YbbR family protein Dhaf_0833 from Desulfito... -

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Basic information

Entry
Database: PDB / ID: 3lyw
TitleCrystal structure of YbbR family protein Dhaf_0833 from Desulfitobacterium hafniense DCB-2. Northeast Structural Genomics Consortium target id DhR29B
ComponentsYbbR family protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / YbbR family protein Dhaf_0833 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyRNA Polymerase Alpha Subunit; Chain A, domain 2 - #30 / YbbR-like / : / YbbR-like protein / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Beta Complex / Mainly Beta / YbbR family protein
Function and homology information
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsSeetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. ...Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of YbbR family protein Dhaf_0833 from Desulfitobacterium hafniense DCB-2. Northeast Structural Genomics Consortium target id DhR29B
Authors: Seetharaman, J. / Lew, S. / Wang, D. / Janjua, H. / Cunningham, K. / Owens, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionFeb 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 6, 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 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YbbR family protein


Theoretical massNumber of molelcules
Total (without water)10,2531
Polymers10,2531
Non-polymers00
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.827, 44.827, 85.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein YbbR family protein


Mass: 10253.337 Da / Num. of mol.: 1 / Fragment: sequence database residues 37-120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: DCB-2 / DSM 10664 / Gene: Dhaf_0833 / Production host: Escherichia coli (E. coli) / References: UniProt: B8FX10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.11 Å3/Da / Density % sol: 41.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 30% PEG3350, sodium acetate 10mM, 5% Glycerol, pH 9, 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 4 / Detector: CCD / Date: Jan 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 15491 / Num. obs: 15491 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17.7 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.054 / Net I/σ(I): 14.5
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 24 / Num. unique all: 768 / Rsym value: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXSphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.9→25.52 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 206005.16 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 773 6 %RANDOM
Rwork0.224 ---
obs0.224 12986 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.7502 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.3 Å20 Å20 Å2
2---5.3 Å20 Å2
3---10.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→25.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms669 0 0 83 752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 121 5.7 %
Rwork0.246 1994 -
obs--95.3 %
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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