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- PDB-1f1e: CRYSTAL STRUCTURE OF THE HISTONE FROM METHANOPYRUS KANDLERI -

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Basic information

Entry
Database: PDB / ID: 1f1e
TitleCRYSTAL STRUCTURE OF THE HISTONE FROM METHANOPYRUS KANDLERI
ComponentsHISTONE FOLD PROTEIN
KeywordsDNA BINDING PROTEIN / Archaeal Histone Protein
Function / homology
Function and homology information


protein heterodimerization activity
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
Histone fold protein
Similarity search - Component
Biological speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.37 Å
AuthorsFahrner, R.L. / Cascio, D. / Lake, J.A. / Slesarev, A.
CitationJournal: Protein Sci. / Year: 2001
Title: An ancestral nuclear protein assembly: crystal structure of the Methanopyrus kandleri histone.
Authors: Fahrner, R.L. / Cascio, D. / Lake, J.A. / Slesarev, A.
History
DepositionMay 18, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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 / struct_site
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 / _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

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Assembly

Deposited unit
A: HISTONE FOLD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2502
Polymers17,2151
Non-polymers351
Water3,171176
1
A: HISTONE FOLD PROTEIN
hetero molecules

A: HISTONE FOLD PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5014
Polymers34,4302
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2410 Å2
ΔGint-40 kcal/mol
Surface area12420 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.40, 57.40, 96.95
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-1002-

HOH

21A-1148-

HOH

DetailsThe biological assembly is a monomer and a dimer created by the crystallographic two fold.

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Components

#1: Protein HISTONE FOLD PROTEIN


Mass: 17214.883 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Plasmid: PLYSS / Production host: Escherichia coli (E. coli) / References: UniProt: O93641
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.3 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein: 18mg/ml HMK, 1M NaCl, 50mM Tris pH 8.5, 50mM BME, Well: 400mM NaCl, 50mM Tris pH 8.5, 50mM BME, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
21 M1dropNaCl
350 mMTris1drop
41 mMbeta-mercaptoethanol1drop
550 mMTris1reservoir
6400 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.78
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 12, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.78 Å / Relative weight: 1
ReflectionResolution: 1.37→30 Å / Num. all: 34781 / Num. obs: 31694 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 17.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.6
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 4 % / Rmerge(I) obs: 0.475 / Num. unique all: 1709 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
SCALEPACKdata scaling
SOLVEphasing
SHELXL-97refinement
RefinementResolution: 1.37→30 Å / Num. parameters: 12837 / Num. restraintsaints: 16871 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: Anisotropic scaling applied by the method of Parkin, Moezzi, and Hope, J. Appl.Cryst. 28(1995)53-56.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 5353 8.5 %RANDOM
Rwork0.159 ---
all0.166 34781 --
obs0.159 31694 16.9 %-
Solvent computationSolvent model: Moews & Kretsinger, J. Mol. Biol. 91(1973)201-228
Refine analyzeNum. disordered residues: 33 / Occupancy sum hydrogen: 1100.02 / Occupancy sum non hydrogen: 1292.63
Refinement stepCycle: LAST / Resolution: 1.37→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1113 0 1 176 1290
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.034
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0228
X-RAY DIFFRACTIONs_zero_chiral_vol0.058
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.077
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.026
X-RAY DIFFRACTIONs_approx_iso_adps0.17
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 8.5 % / Rfactor obs: 0.163 / Rfactor Rfree: 0.208
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.88

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