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- PDB-1j8b: Structure of YbaB from Haemophilus influenzae (HI0442), a protein... -

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Basic information

Entry
Database: PDB / ID: 1j8b
TitleStructure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function
ComponentsYbaB
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HI0442 / hypothetical protein / Structure 2 Function Project / S2F
Function / homology
Function and homology information


bacterial nucleoid / DNA binding / cytosol
Similarity search - Function
Nucleoid-associated protein YbaB-like domain / Nucleoid-associated protein YbaB/EbfC family / YbaB/EbfC DNA-binding family / Ybab; Chain: A; / Nucleoid-associated protein YbaB-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoid-associated protein HI_0442
Similarity search - Component
Biological speciesHaemophilus influenzae Rd (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsLim, K. / Tempcyzk, A. / Toedt, J. / Parsons, J.F. / Howard, A. / Eisenstein, E. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2003
Title: Crystal structure of YbaB from Haemophilus influenzae (HI0442), a protein of unknown function coexpressed with the recombinational DNA repair protein RecR
Authors: Lim, K. / Tempcyzk, A. / Parsons, J.F. / Bonander, N. / Toedt, J. / Kelman, Z. / Howard, A. / Eisenstein, E. / Herzberg, O.
History
DepositionMay 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Sep 26, 2012Group: Database references
Revision 1.4Oct 30, 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: YbaB


Theoretical massNumber of molelcules
Total (without water)12,7341
Polymers12,7341
Non-polymers00
Water2,900161
1
A: YbaB

A: YbaB


Theoretical massNumber of molelcules
Total (without water)25,4682
Polymers25,4682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+3/21
Unit cell
Length a, b, c (Å)44.39, 132.79, 36.22
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-324-

HOH

21A-336-

HOH

DetailsTo obtain a dimer, apply -X,Y,1/2-Z symmetry operator and 1,0,1 translation vector

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Components

#1: Protein YbaB / HYPOTHETICAL PROTEIN HI0442


Mass: 12734.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae Rd (bacteria) / Species: Haemophilus influenzae / Strain: KW20 / Gene: HI0442 / Plasmid: pET15b-HI0442 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P44711
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.09 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 3.8
Details: 1 M ammonium phosphate, pH 3.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113 mg/mlprotein1drop
250 mMTris1droppH7.5
30.1 mMdithiothreitol1drop
40.1 mMEDTA1drop
50.9-1.1 Mammonium phosphate monobasic1reservoirpH3.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.9789, 0.9790, 0.9500
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 1, 2000
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.9791
30.951
ReflectionResolution: 1.75→99 Å / Num. all: 10936 / Num. obs: 10936 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 18
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.214 / Num. unique all: 810 / % possible all: 73.5
Reflection
*PLUS
Lowest resolution: 99 Å / Num. obs: 19416 / Num. measured all: 73832 / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 73.5 % / Rmerge(I) obs: 0.201

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHELXmodel building
MLPHAREphasing
DMmodel building
CNSrefinement
SHELXphasing
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→99 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.263 1093 10.2 %random
Rwork0.18 ---
all-10912 --
obs-10681 --
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 1.75→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 0 0 161 863
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_angle_deg1.8
LS refinement shellResolution: 1.75→1.83 Å /
Rfactor% reflection
Rfree0.301 -
Rwork0.348 -
obs-77.3 %
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / Rfactor Rfree: 0.274 / Rfactor Rwork: 0.185
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.331 / Rfactor Rwork: 0.353

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