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- PDB-1a7w: CRYSTAL STRUCTURE OF THE HISTONE HMFB FROM METHANOTHERMUS FERVIDUS -

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Basic information

Entry
Database: PDB / ID: 1a7w
TitleCRYSTAL STRUCTURE OF THE HISTONE HMFB FROM METHANOTHERMUS FERVIDUS
ComponentsHISTONE HMFB
KeywordsHISTONE
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 / 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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 HMFB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7843
Polymers7,6831
Non-polymers1012
Water82946
1
A: HISTONE HMFB
hetero molecules

A: HISTONE HMFB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5686
Polymers15,3662
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3620 Å2
ΔGint-95 kcal/mol
Surface area7480 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)31.300, 61.580, 39.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein HISTONE HMFB


Mass: 7683.054 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermus fervidus (archaea) / Gene: HMFB / Gene (production host): HMFB / Production host: Escherichia coli (E. coli) / References: UniProt: P19267
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.5 Å3/Da / Density % sol: 51 %
Description: ORTHOROMBIC HMFA STRUCTURE WILL BE SUBMITTED SOON
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: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Feb 1, 1995 / Details: SUPPER NI-COATED MIRROR SYSTEM
RadiationMonochromator: NI FOIL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→39.1 Å / Num. obs: 6152 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 22.87 Å2 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 8.3
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.196 / % possible all: 97.2
Reflection
*PLUS
Num. measured all: 25200
Reflection shell
*PLUS
% possible obs: 97.2 %

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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) : 0.25
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: 0.25 Å
Refinement stepCycle: LAST / Resolution: 1.55→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms527 0 2 46 575
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Num. reflection obs: 5835 / Num. reflection Rfree: 290 / Rfactor obs: 0.18 / Rfactor Rfree: 0.229
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d0.037
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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