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- PDB-3cb6: Crystal Structure of the S. pombe Peptidase Homology Domain of FA... -

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Basic information

Entry
Database: PDB / ID: 3cb6
TitleCrystal Structure of the S. pombe Peptidase Homology Domain of FACT complex subunit Spt16 (form B)
ComponentsFACT complex subunit spt16FACT (biology)
KeywordsTRANSCRIPTION / peptidase homology domain / histone binding module / histone H3/H4 chaperone / pita-bread fold / Chromosomal protein / DNA damage / DNA repair / DNA replication / Nucleus / Transcription regulation
Function / homology
Function and homology information


H2A-H2B histone complex chaperone activity / Regulation of TP53 Activity through Phosphorylation / constitutive heterochromatin formation / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / FACT complex / histone chaperone activity / nucleosome organization / DNA replication-dependent chromatin assembly ...H2A-H2B histone complex chaperone activity / Regulation of TP53 Activity through Phosphorylation / constitutive heterochromatin formation / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Elongation / FACT complex / histone chaperone activity / nucleosome organization / DNA replication-dependent chromatin assembly / transcription elongation-coupled chromatin remodeling / nucleosome binding / transcription elongation by RNA polymerase II / euchromatin / chromatin organization / DNA replication / DNA repair / nucleus
Similarity search - Function
: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like 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 ...: / FACT complex subunit SPT16, C-terminal domain / FACT complex subunit Spt16, peptidase M24-like 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 / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / PH-like domain superfamily / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FACT complex subunit spt16
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsStuwe, T. / Hothorn, M. / Lejeune, E. / Bortfeld-Miller, M. / Scheffzek, K. / Ladurner, A.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: The FACT Spt16 "peptidase" domain is a histone H3-H4 binding module
Authors: Stuwe, T. / Hothorn, M. / Lejeune, E. / Rybin, V. / Bortfeld, M. / Scheffzek, K. / Ladurner, A.G.
History
DepositionFeb 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 17, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FACT complex subunit spt16


Theoretical massNumber of molelcules
Total (without water)49,9881
Polymers49,9881
Non-polymers00
Water6,341352
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: FACT complex subunit spt16

A: FACT complex subunit spt16


Theoretical massNumber of molelcules
Total (without water)99,9762
Polymers99,9762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area38410 Å2
ΔGint-8.5 kcal/mol
Surface area1820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.980, 193.670, 89.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-749-

HOH

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Components

#1: Protein FACT complex subunit spt16 / FACT (biology) / Facilitates chromatin transcription complex subunit spt16


Mass: 49987.773 Da / Num. of mol.: 1 / Fragment: N-terminal fragment, UNP residues 1-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (fission yeast)
Gene: spt16 / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: O94267
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.73 Å3/Da / Density % sol: 54.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 300, 0.1M Mes, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9699 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9699 Å / Relative weight: 1
ReflectionResolution: 1.84→19.85 Å / Num. all: 47917 / Num. obs: 47711 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.058 / Net I/σ(I): 20.49
Reflection shellResolution: 1.84→1.95 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 7564 / Rsym value: 0.373 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.4.0067refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CB5

3cb5


Resolution: 1.84→19.85 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.934 / SU B: 5.435 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.129 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22472 2386 5 %RANDOM
Rwork0.19209 ---
all0.193 45322 --
obs0.19371 45322 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.018 Å2
Baniso -1Baniso -2Baniso -3
1-1.99 Å20 Å20 Å2
2---0.88 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 1.84→19.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3475 0 0 352 3827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223549
X-RAY DIFFRACTIONr_bond_other_d0.0010.022415
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9694800
X-RAY DIFFRACTIONr_angle_other_deg1.30235929
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.495444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.77925.032157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57515647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.0381515
X-RAY DIFFRACTIONr_chiral_restr0.080.2547
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02691
X-RAY DIFFRACTIONr_mcbond_it0.6511.52197
X-RAY DIFFRACTIONr_mcbond_other0.1831.5896
X-RAY DIFFRACTIONr_mcangle_it1.19923548
X-RAY DIFFRACTIONr_scbond_it2.01831352
X-RAY DIFFRACTIONr_scangle_it3.2164.51250
LS refinement shellResolution: 1.84→1.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 169 -
Rwork0.276 3213 -
obs--100 %
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)
12.44120.639-0.23821.6046-0.41631.3930.0076-0.0296-0.13960.0490.01650.07140.1214-0.0236-0.0241-0.0126-0.02820.006-0.13490.0008-0.1114-7.128113.3127-4.9883
20.74880.69680.02333.2701-0.021.43580.02090.02550.0338-0.0384-0.0141-0.07410.00850.0643-0.0069-0.2334-0.006-0.0069-0.10510.0085-0.140213.007241.7271-0.4694
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-1 - 1701 - 172
2X-RAY DIFFRACTION2AA171 - 439173 - 441

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