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- PDB-1ku5: Crystal Structure of recombinant histone HPhA from hyperthermophi... -

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Basic information

Entry
Database: PDB / ID: 1ku5
TitleCrystal Structure of recombinant histone HPhA from hyperthermophilic archaeon Pyrococcus horikoshii OT3
ComponentsHPhA
KeywordsDNA BINDING PROTEIN / HISTONE FOLD
Function / homology
Function and homology information


chromosome / protein heterodimerization activity / DNA binding / cytoplasm
Similarity search - Function
: / : / Transcription factor CBF/NF-Y/archaeal histone domain / Histone-like transcription factor (CBF/NF-Y) and archaeal histone / Histone, subunit A / Histone, subunit A / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Archaeal histone A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLi, T. / Sun, F. / Ji, X. / Feng, Y. / Rao, Z.
Citation
Journal: J.MOL.BIOL. / Year: 2003
Title: Structure based hyperthermostability of archaeal histone HPhA from Pyrococcus horikoshii
Authors: Li, T. / Sun, F. / Ji, X. / Feng, Y. / Rao, Z.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2002
Title: Crystallization and preliminary X-ray analysis of recombinant histone HPhA from the hyperthermophilic archaeon Pyrococcus horikoshii OT3
Authors: Li, T. / Ji, X. / Sun, F. / Gao, R. / Cao, S. / Feng, Y. / Rao, Z.
History
DepositionJan 21, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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: HPhA
B: HPhA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0386
Polymers15,7652
Non-polymers2734
Water64936
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-56 kcal/mol
Surface area6910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.993, 46.887, 35.023
Angle α, β, γ (deg.)90.00, 103.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HPhA / archaeal histone


Mass: 7882.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O74098
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 1.58 Å3/Da / Density % sol: 29.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, PEG4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1100 mM1reservoirpH4.6NaAc
219 %(w/v)PEG40001reservoir
30.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2001 / Details: Osmic mirrors
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→100 Å / Num. all: 5028 / Num. obs: 4932 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 18.46 Å2 / Rmerge(I) obs: 0.063
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.185 / Num. unique all: 437 / % possible all: 88.5

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Processing

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

1hta


Resolution: 2.3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 386 10 %RANDOM
Rwork0.216 ---
all-4960 --
obs-4880 90.6 %-
Displacement parametersBiso mean: 22.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.7 Å20 Å22.5 Å2
2---5.6 Å20 Å2
3---1.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.356 Å0.268 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1028 0 17 36 1081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.98
X-RAY DIFFRACTIONc_improper_angle_d0.803
X-RAY DIFFRACTIONc_bond_d0.00619
X-RAY DIFFRACTIONc_dihedral_angle_d19.3
LS refinement shellResolution: 2.3→2.38 Å
RfactorNum. reflection% reflection
Rfree0.225 38 -
Rwork0.197 --
obs-437 88.5 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3hac_so4.param
X-RAY DIFFRACTION4water.param
Refinement
*PLUS
Rfactor Rfree: 0.273 / Rfactor Rwork: 0.207
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0109
X-RAY DIFFRACTIONc_angle_deg1.2546
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.803

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