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- PDB-1nh9: Crystal Structure of a DNA Binding Protein Mja10b from the hypert... -

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Basic information

Entry
Database: PDB / ID: 1nh9
TitleCrystal Structure of a DNA Binding Protein Mja10b from the hyperthermophile Methanococcus jannaschii
ComponentsDNA-binding protein Alba
KeywordsDNA BINDING PROTEIN / Mja10b
Function / homology
Function and homology information


chromosome condensation / chromosome / double-stranded DNA binding / RNA binding / cytoplasm
Similarity search - Function
DNA/RNA-binding protein Alba / Alba-like domain / DNA/RNA-binding protein Alba-like / Alba / Alba-like domain superfamily / Translation Initiation Factor IF3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA/RNA-binding protein Alba
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWang, G. / Bartlam, M. / Guo, R. / Yang, H. / Xue, H. / Liu, Y. / Huang, L. / Rao, Z.
CitationJournal: Protein Sci. / Year: 2003
Title: Crystal structure of a DNA binding protein from the hyperthermophilic euryarchaeon Methanococcus jannaschii
Authors: Wang, G. / Guo, R. / Bartlam, M. / Yang, H. / Xue, H. / Liu, Y. / Huang, L. / Rao, Z.
History
DepositionDec 19, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-binding protein Alba


Theoretical massNumber of molelcules
Total (without water)9,6911
Polymers9,6911
Non-polymers00
Water43224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.506, 51.506, 125.307
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe biological assembly is a monomer in the asymmetric unit

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Components

#1: Protein DNA-binding protein Alba / Mja10b


Mass: 9690.525 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q57665
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.73 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.25
Details: Tris-HCl, MPD, pH 8.25, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: Wang, G.G., (2002) Acta Cryst., D58, 1240.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
240 %MPD1reservoir
30.1 MTris-HCl1reservoirpH8.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9868 Å
DetectorType: SBC-2 / Detector: CCD / Date: Apr 15, 2002 / Details: mirrors
RadiationMonochromator: sagitally focused Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9868 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 7093 / Num. obs: 7093 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 21.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.2 / Num. unique all: 692 / % possible all: 99.1
Reflection
*PLUS
Num. obs: 6946 / % possible obs: 96.6 % / Redundancy: 13.1 % / Num. measured all: 91002 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.06 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1h0x

1h0x


Resolution: 2→20 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: overall / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 678 10 %random
Rwork0.209 ---
obs-6217 94.2 %-
Displacement parametersBiso mean: 40.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.818 Å2-1.751 Å20 Å2
2---0.818 Å20 Å2
3---1.635 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.14 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms619 0 0 24 643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 2→2.06 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 12
RfactorNum. reflection% reflection
Rfree0.288 121 10.7 %
Rwork0.263 761 -
obs-1298 81.1 %
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.405
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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