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

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Basic information

Entry
Database: PDB / ID: 1hta
TitleCRYSTAL STRUCTURE OF THE HISTONE HMFA FROM METHANOTHERMUS FERVIDUS
ComponentsHISTONE HMFA
KeywordsHISTONE
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: 1.55 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 Hyperthermophile, Methanothermus Fervidus, Confirms that This Archaeal Protein is a Histone
Authors: Starich, M.R. / Sandman, K. / Reeve, J.N. / Summers, M.F.
History
DepositionMar 18, 1998Processing site: BNL
Revision 1.0Mar 23, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: 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: HISTONE HMFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,5492
Polymers7,5141
Non-polymers351
Water1,00956
1
A: HISTONE HMFA
hetero molecules

A: HISTONE HMFA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0994
Polymers15,0282
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3550 Å2
ΔGint-45 kcal/mol
Surface area7160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)41.700, 41.700, 81.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein HISTONE HMFA


Mass: 7513.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Gene: HMFA / Plasmid: PKS354 / Gene (production host): HMFB / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / References: UniProt: P48781
#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.: 56 / 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: 2.4 Å3/Da / Density % sol: 40 %
Description: ORTHOROMBIC HMFA STRUCTURE WILL BE SUBMITTED SOON

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.937
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1995 / Details: SEGMENTED MIRROR
RadiationMonochromator: BENT SINGLE-CRYSTAL GERMANIUM TRIANGULAR MONOCHROMATOR
Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.937 Å / Relative weight: 1
ReflectionResolution: 1.55→37.3 Å / Num. obs: 10817 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 22.87 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 4.8
Reflection shellResolution: 1.55→1.6 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3 / Rsym value: 0.247 / % possible all: 99

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED ORTHORHOMBIC HMFA

Resolution: 1.55→18 Å / Cross valid method: AFTER RIGID BODY REFINEMENT / σ(F): 0
Details: RIGID BODY WITH AMORE, SIMULATED ANNEALING WITH X-PLOR, REFINEMENT WITH REFMAC. ESD FROM LUZZATI PLOT (A) : 0.2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 520 5 %RANDOM
Rwork0.198 ---
obs0.2 10797 97.4 %-
Displacement parametersBiso mean: 25.34 Å2
Baniso -1Baniso -2Baniso -3
1-1.398 Å21.398 Å20 Å2
2--0 Å2-2.69 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.55→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms508 0 1 56 565
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0220.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9322
X-RAY DIFFRACTIONp_mcangle_it2.6763
X-RAY DIFFRACTIONp_scbond_it3.4262
X-RAY DIFFRACTIONp_scangle_it5.2413
X-RAY DIFFRACTIONp_plane_restr0.02420.03
X-RAY DIFFRACTIONp_chiral_restr0.1610.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.30.3
X-RAY DIFFRACTIONp_xhyhbond_nbd0.3
X-RAY DIFFRACTIONp_xyhbond_nbd0.3
X-RAY DIFFRACTIONp_planar_tor3.97
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor4.520
X-RAY DIFFRACTIONp_special_tor015

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