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- PDB-2z7c: Crystal structure of chromatin protein alba from hyperthermophili... -

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Basic information

Entry
Database: PDB / ID: 2z7c
TitleCrystal structure of chromatin protein alba from hyperthermophilic archaeon pyrococcus horikoshii
ComponentsDNA/RNA-binding protein Alba
KeywordsDNA BINDING PROTEIN / RNA BINDING PROTEIN / alba / DNA/RNA binding / Acetylation / Cytoplasm / DNA-binding / RNA-binding
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
ARGININE / DNA/RNA-binding protein Alba
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHada, K. / Nakashima, T. / Osawa, T. / Shimada, H. / Kakuta, Y. / Kimura, M.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2008
Title: Crystal structure and functional analysis of an archaeal chromatin protein Alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3.
Authors: Hada, K. / Nakashima, T. / Osawa, T. / Shimada, H. / Kakuta, Y. / Kimura, M.
History
DepositionAug 17, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 22, 2019Group: Data collection / Category: reflns / Item: _reflns.B_iso_Wilson_estimate
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA/RNA-binding protein Alba
B: DNA/RNA-binding protein Alba
C: DNA/RNA-binding protein Alba
D: DNA/RNA-binding protein Alba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9466
Polymers41,5964
Non-polymers3502
Water1,54986
1
A: DNA/RNA-binding protein Alba
B: DNA/RNA-binding protein Alba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9733
Polymers20,7982
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-10 kcal/mol
Surface area10150 Å2
MethodPISA
2
C: DNA/RNA-binding protein Alba
D: DNA/RNA-binding protein Alba
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9733
Polymers20,7982
Non-polymers1751
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-10 kcal/mol
Surface area10320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.262, 51.974, 173.004
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR DETERMINED THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein
DNA/RNA-binding protein Alba


Mass: 10398.988 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Strain: OT3 / Gene: PHS053 / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) codonplus RIL / References: UniProt: O74101
#2: Chemical ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.21 Å3/Da / Density % sol: 44.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 15% PEGMME 550, 0.2M Sodium chloride, 0.1M Bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 16, 2007 / Details: vertically bent cylinder mirror coated in Rhodium
RadiationMonochromator: Si(511) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.79→50 Å / Num. obs: 8238 / % possible obs: 83.1 % / Observed criterion σ(F): 0 / Redundancy: 5.1 % / Rsym value: 0.168
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.4 % / Num. unique all: 496 / Rsym value: 0.374 / % possible all: 51

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Y9X

1y9x


Resolution: 2.8→44.55 Å / Rfactor Rfree error: 0.016 / Data cutoff high absF: 1695985.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.318 420 5.1 %RANDOM
Rwork0.23 ---
obs0.23 8182 84 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.1912 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 60.1 Å2
Baniso -1Baniso -2Baniso -3
1-44.8 Å20 Å20 Å2
2---14.17 Å20 Å2
3----30.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2833 0 0 86 2919
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.681.5
X-RAY DIFFRACTIONc_mcangle_it32
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.992.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.439 57 6.5 %
Rwork0.363 817 -
obs--55.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ligand.paramligand.top

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