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- PDB-4khb: Structure of the Spt16D Pob3N heterodimer -

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Basic information

Entry
Database: PDB / ID: 4khb
TitleStructure of the Spt16D Pob3N heterodimer
Components
  • Uncharacterized protein POB3N
  • Uncharacterized protein SPT16D
KeywordsTRANSCRIPTION/REPLICATION / PH like domains / TRANSCRIPTION-REPLICATION complex
Function / homology
Function and homology information


FACT complex / chromosome / DNA replication / DNA repair / DNA binding / nucleus / metal ion binding
Similarity search - Function
FACT complex subunit Spt16p/Cdc68p / Structure-specific recognition protein (SSRP1) / : / SSRP1 PH domain / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain ...FACT complex subunit Spt16p/Cdc68p / Structure-specific recognition protein (SSRP1) / : / SSRP1 PH domain / FACT complex subunit Spt16, peptidase M24-like domain / : / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit SSRP1/POB3 / SSRP1, dimerization domain / FACT complex subunit SSRP1/POB3, N-terminal PH domain / SSRP1 domain superfamily / : / Structure-specific recognition protein (SSRP1) / POB3-like N-terminal PH domain / FACT complex subunit Spt16 domain / FACT complex subunit (SPT16/CDC68) / FACT complex subunit (SPT16/CDC68) / FACT complex subunit Spt16, N-terminal lobe domain / FACT complex subunit Spt16 / FACT complex subunit SPT16 N-terminal lobe domain / FACT complex subunit SPT16 N-terminal lobe domain / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FACT complex subunit / FACT complex subunit POB3
Similarity search - Component
Biological speciesChaetomium thermophilum var. thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsStuwe, T. / Zhang, E. / Ladurner, A.G.
CitationJournal: Nature / Year: 2013
Title: Structural basis of histone H2A-H2B recognition by the essential chaperone FACT.
Authors: Hondele, M. / Stuwe, T. / Hassler, M. / Halbach, F. / Bowman, A. / Zhang, E.T. / Nijmeijer, B. / Kotthoff, C. / Rybin, V. / Amlacher, S. / Hurt, E. / Ladurner, A.G.
History
DepositionApr 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2Jul 17, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein SPT16D
D: Uncharacterized protein POB3N
F: Uncharacterized protein POB3N
H: Uncharacterized protein POB3N
G: Uncharacterized protein SPT16D
E: Uncharacterized protein SPT16D
C: Uncharacterized protein SPT16D
B: Uncharacterized protein POB3N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,08017
Polymers146,2168
Non-polymers8659
Water4,774265
1
A: Uncharacterized protein SPT16D
B: Uncharacterized protein POB3N
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8425
Polymers36,5542
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-32 kcal/mol
Surface area14940 Å2
MethodPISA
2
D: Uncharacterized protein POB3N
C: Uncharacterized protein SPT16D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8425
Polymers36,5542
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-34 kcal/mol
Surface area13890 Å2
MethodPISA
3
F: Uncharacterized protein POB3N
E: Uncharacterized protein SPT16D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7464
Polymers36,5542
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-67 kcal/mol
Surface area14220 Å2
MethodPISA
4
H: Uncharacterized protein POB3N
G: Uncharacterized protein SPT16D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6503
Polymers36,5542
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4710 Å2
ΔGint-62 kcal/mol
Surface area13680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.391, 128.082, 132.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsheterodimer

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Components

#1: Protein
Uncharacterized protein SPT16D


Mass: 14720.704 Da / Num. of mol.: 4 / Fragment: UNP residues 522-647
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0052370, Spt16 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SDN1
#2: Protein
Uncharacterized protein POB3N


Mass: 21833.240 Da / Num. of mol.: 4 / Fragment: UNP residues 1-192
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum var. thermophilum (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0070340, Pob3 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHK5
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 5.6
Details: 2.2M NH4SO4, 0.2M Na-K-tatrate, 0.2M Na3citrate pH 5.6, VAPOR DIFFUSION, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→47.8 Å / Num. obs: 57453 / % possible obs: 99.9 % / Observed criterion σ(I): 1.9 / Biso Wilson estimate: 43.14 Å2
Reflection shellResolution: 2.4→2.5 Å / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
DNAdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→47.778 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8163 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 25.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2435 2873 5 %
Rwork0.202 --
obs0.2043 57449 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.15 Å2 / Biso mean: 24.4568 Å2 / Biso min: 0 Å2
Refinement stepCycle: LAST / Resolution: 2.4→47.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8981 0 45 265 9291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049296
X-RAY DIFFRACTIONf_angle_d0.91212525
X-RAY DIFFRACTIONf_chiral_restr0.0611293
X-RAY DIFFRACTIONf_plane_restr0.0031638
X-RAY DIFFRACTIONf_dihedral_angle_d17.723444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.4-2.43940.30971160.271526232739
2.4394-2.48140.34971450.273325282673
2.4814-2.52650.35541320.268725612693
2.5265-2.57510.30121420.266525682710
2.5751-2.62770.3461420.265825442686
2.6277-2.68480.2981510.24825362687
2.6848-2.74730.30681430.255926042747
2.7473-2.8160.331320.248825522684
2.816-2.89210.28721370.233725512688
2.8921-2.97720.29031360.239326102746
2.9772-3.07330.24061450.219825662711
3.0733-3.18310.26941210.212425912712
3.1831-3.31050.26661280.212525942722
3.3105-3.46110.23111350.207725862721
3.4611-3.64350.22921490.199925932742
3.6435-3.87170.18951170.17626262743
3.8717-4.17050.19651360.168326102746
4.1705-4.58990.20481440.153826272771
4.5899-5.25340.19741340.159926502784
5.2534-6.61590.25031320.20926772809
6.6159-47.7870.23131560.196227792935

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