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- PDB-9f2c: Archaeal histone protein HTkC from Thermococcus kodakarensis -

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Basic information

Entry
Database: PDB / ID: 9f2c
TitleArchaeal histone protein HTkC from Thermococcus kodakarensis
Componentshypothetical protein
KeywordsDNA BINDING PROTEIN / Archaeal histone
Function / homologyHistone-fold / protein heterodimerization activity / Uncharacterized protein
Function and homology information
Biological speciesThermococcus kodakarensis (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsHu, Y. / Albrecht, R. / Hartmann, M.D.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2024
Title: Histones and histone variant families in prokaryotes.
Authors: Schwab, S. / Hu, Y. / van Erp, B. / Cajili, M.K.M. / Hartmann, M.D. / Hernandez Alvarez, B. / Alva, V. / Boyle, A.L. / Dame, R.T.
History
DepositionApr 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
B: hypothetical protein
C: hypothetical protein
D: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)27,0604
Polymers27,0604
Non-polymers00
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-77 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.655, 64.294, 79.846
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
/ NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
hypothetical protein


Mass: 6764.946 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK1040 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JDW7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 50.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.01 M trisodium citrate and 33% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→44 Å / Num. obs: 24121 / % possible obs: 99.6 % / Redundancy: 7.16 % / CC1/2: 0.998 / Rrim(I) all: 0.107 / Net I/σ(I): 12.63
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 7.15 % / Mean I/σ(I) obs: 1.36 / Num. unique obs: 3815 / CC1/2: 0.655 / Rrim(I) all: 1.48 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.8.0266refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→44 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.864 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23649 1205 5 %RANDOM
Rwork0.20348 ---
obs0.20508 22916 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.242 Å2
Baniso -1Baniso -2Baniso -3
1-1.4 Å20 Å2-0 Å2
2---0.78 Å20 Å2
3----0.63 Å2
Refinement stepCycle: 1 / Resolution: 1.84→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1789 0 0 203 1992
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131820
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171814
X-RAY DIFFRACTIONr_angle_refined_deg1.2631.6562448
X-RAY DIFFRACTIONr_angle_other_deg1.2641.5854168
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.295228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.45720.90988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.26715344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0061515
X-RAY DIFFRACTIONr_chiral_restr0.0560.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022023
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.792.173918
X-RAY DIFFRACTIONr_mcbond_other0.7882.172917
X-RAY DIFFRACTIONr_mcangle_it1.2653.2491141
X-RAY DIFFRACTIONr_mcangle_other1.2643.251142
X-RAY DIFFRACTIONr_scbond_it1.0912.357902
X-RAY DIFFRACTIONr_scbond_other1.092.357902
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8313.4671306
X-RAY DIFFRACTIONr_long_range_B_refined4.18926.4622036
X-RAY DIFFRACTIONr_long_range_B_other3.92625.5381976
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A16050.12
12B16050.12
21A16860.12
22C16860.12
31A16260.07
32D16260.07
41B15910.09
42C15910.09
51B16170.1
52D16170.1
61C16100.08
62D16100.08
LS refinement shellResolution: 1.84→1.886 Å
RfactorNum. reflection% reflection
Rfree0.398 86 -
Rwork0.423 1652 -
obs--98.3 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.55290.6994-2.27381.1323-1.75645.1228-0.1109-0.0138-0.1133-0.041-0.0201-0.00910.17420.04230.13090.0760.0208-0.02580.0077-0.01160.0301-13.152514.4279-3.2923
21.2567-0.2835-1.75510.62120.34293.674-0.0927-0.0581-0.0881-0.01250.0145-0.00380.15820.12860.07830.0855-0.0224-0.02990.02040.02550.0439-12.493314.6217-2.1688
33.4626-1.3223-3.13521.54071.674.36830.1063-0.04190.1624-0.0795-0.07360.0351-0.29930.0042-0.03270.1127-0.0197-0.02990.0135-0.00460.026-9.101735.8303-2.3484
43.09570.5725-2.82850.8067-0.30873.35720.111-0.01720.10850.0277-0.0671-0.0161-0.3334-0.0572-0.04390.12730.0055-0.01930.0126-0.00210.0119-10.905636.0108-1.9998
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 59
2X-RAY DIFFRACTION2B3 - 59
3X-RAY DIFFRACTION3C2 - 59
4X-RAY DIFFRACTION4D3 - 59

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