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- PDB-1b6w: CRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB... -

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Basic information

Entry
Database: PDB / ID: 1b6w
TitleCRYSTAL STRUCTURE OF THE SELENOMETHIONINE VARIANT OF HISTONE HMFB FROM METHANOTHERMUS FERVIDUS
ComponentsPROTEIN (HISTONE HMFB)
KeywordsDNA BINDING PROTEIN / HISTONE / HMF-2 / ARCHAEAL HISTONE B
Function / homology
Function and homology information


DNA topological change / protein homooligomerization / 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-2
Similarity search - Component
Biological speciesMethanothermus fervidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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: Derived calculations / 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_conn / struct_ref_seq_dif
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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HISTONE HMFB)


Theoretical massNumber of molelcules
Total (without water)7,7771
Polymers7,7771
Non-polymers00
Water25214
1
A: PROTEIN (HISTONE HMFB)

A: PROTEIN (HISTONE HMFB)


Theoretical massNumber of molelcules
Total (without water)15,5542
Polymers15,5542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3280 Å2
ΔGint-32 kcal/mol
Surface area7730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)29.990, 60.330, 74.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (HISTONE HMFB)


Mass: 7776.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: THIS IS A SELENOMETHIONINE PROTEIN. RESIDUES 1 AND 35 ARE SEMET (BUT SIDE CHAIN OF RESIDUE 1 IS DISORDERED)
Source: (gene. exp.) Methanothermus fervidus (archaea) / Gene: HMFB / Production host: Escherichia coli (E. coli) / References: UniProt: P19267
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.18 Å3/Da / Density % sol: 43.48 %
Description: ORTHOROMBIC HMFA STRUCTURE WILL BE SUBMITTED SOON
Crystal growpH: 6.5 / Details: 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 citrate1drop
350 mMTris-HCl1drop
40.1 MMES1reservoir
50.2 Mammonium sulfate1reservoir
630 %(w/v)PEG5000 MME1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 0.877
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: IMAGE PLATE 18 CM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.877 Å / Relative weight: 1
ReflectionResolution: 2.05→14 Å / Num. obs: 11343 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rsym value: 8.8 / Net I/σ(I): 4.1
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3.2 / Rsym value: 20 / % possible all: 65.8
Reflection
*PLUS
Highest resolution: 2.05 Å / % possible obs: 97.2 % / Rmerge(I) obs: 0.086
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.17 Å / % possible obs: 90.2 % / Rmerge(I) obs: 0.158

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Processing

Software
NameVersionClassification
AMoRE(CCP4)phasing
REFMACrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
SCALAdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PARTIALLY REFINED ORTHORHOMBIC HMFA

Resolution: 2.05→18 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.26 185 5 %RANDOM
Rwork0.21 ---
obs0.21 4171 92 %-
Refinement stepCycle: LAST / Resolution: 2.05→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms516 0 0 14 530
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.013
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.041
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.21 / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

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