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- PDB-1b67: CRYSTAL STRUCTURE OF THE HISTONE HMFA FROM METHANOTHERMUS FERVIDUS -

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Basic information

Entry
Database: PDB / ID: 1b67
TitleCRYSTAL STRUCTURE OF THE HISTONE HMFA FROM METHANOTHERMUS FERVIDUS
ComponentsPROTEIN (HISTONE HMFA)
KeywordsDNA BINDING PROTEIN / HISTONE / HMF1
Function / homology
Function and homology information


DNA topological change / chromosome / double-stranded DNA binding / protein heterodimerization activity / protein homodimerization activity / 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
DNA-binding protein HMf-1
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsDecanniere, K. / Sandman, K. / Reeve, J.N. / Heinemann, U.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus.
Authors: Decanniere, K. / Babu, A.M. / Sandman, K. / Reeve, J.N. / Heinemann, U.
#1: Journal: Proteins / Year: 1996
Title: Crystallization and Preliminary X-Ray Characterization of the Methanothermus Fervidus Histones Hmfa and Hmfb
Authors: Decanniere, K. / Sandman, K. / Reeve, J.N. / Heinemann, U.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: NMR Structure of Hmfb from the Hyperthermophyle, Methanothermus Fervidus, Confirms that This Archaeal Protein is a Histone
Authors: Starich, M.R. / Sandman, K. / Reeve, J.N. / Summers, M.F.
History
DepositionJan 19, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 17, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HISTONE HMFA)
B: PROTEIN (HISTONE HMFA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8613
Polymers14,7652
Non-polymers961
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-47 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.720, 52.580, 67.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.09063, 0.2457, 0.9651), (0.27352, -0.92568, 0.26135), (0.95759, 0.28765, 0.01669)
Vector: -17.34369, 28.27693, 8.62265)

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Components

#1: Protein PROTEIN (HISTONE HMFA)


Mass: 7382.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Gene: HMFA / Plasmid: PKS354 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P48781
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.03 Å3/Da / Density % sol: 39.28 %
Crystal growpH: 6.5
Details: CRYSTALLISATION IN HANGING DROP RESERVOIR: 2.6 M (NH4)2SO4 PROTEIN WAS MIXED 1 TO 1 WITH RESERVOIR SOLUTION, pH 6.5
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-20 mg/mlprotein1drop
2100 mMpotassium citrate1reservoir
350 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.48→11 Å / Num. obs: 77006 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rsym value: 5.7 / Net I/σ(I): 2.9
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.9 / Rsym value: 25.6 / % possible all: 100
Reflection
*PLUS
Num. obs: 20445 / Num. measured all: 77006 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.256

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Processing

Software
NameVersionClassification
AMoRE(CCP4)phasing
SHELXL-97refinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NMR MODEL OF HMFB

Resolution: 1.48→11 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: REFINEMENT AGAINST I'S
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1044 5 %RANDOM
all0.193 20400 --
obs0.188 -99 %-
Refinement stepCycle: LAST / Resolution: 1.48→11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1002 0 5 77 1084
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.028
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.054
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.8 Å2
Refine LS restraints
*PLUS
Type: s_planar_d / Dev ideal: 0.054

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