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- PDB-3f5r: The crystal structure of a subunit of the heterodimeric FACT comp... -

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Basic information

Entry
Database: PDB / ID: 3f5r
TitleThe crystal structure of a subunit of the heterodimeric FACT complex (Spt16p-Pob3p).
ComponentsFACT complex subunit POB3
Keywordstranscription regulator / APC7736 / FACT complex (Spt16p-Pob3p) / Saccharomyces cerevisiae / structural genomics / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / Chromosomal protein / DNA damage / DNA repair / DNA replication / Nucleus / Phosphoprotein / Transcription / Transcription regulation
Function / homology
Function and homology information


Regulation of TP53 Activity through Phosphorylation / FACT complex / regulation of chromatin organization / nucleosome organization / replication fork protection complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA-templated DNA replication / chromatin organization ...Regulation of TP53 Activity through Phosphorylation / FACT complex / regulation of chromatin organization / nucleosome organization / replication fork protection complex / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Pre-transcription Events / positive regulation of RNA polymerase II transcription preinitiation complex assembly / DNA-templated DNA replication / chromatin organization / DNA repair / chromatin / DNA binding
Similarity search - Function
: / SSRP1 PH 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 / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain ...: / SSRP1 PH 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 / Histone chaperone RTT106/FACT complex subunit SPT16-like, middle domain / Histone chaperone Rttp106-like, middle domain / Histone chaperone Rttp106-like / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
FORMIC ACID / FACT complex subunit POB3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsTan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a subunit of the heterodimeric FACT complex (Spt16p-Pob3p).
Authors: Tan, K. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionNov 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 27, 2023Group: 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.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FACT complex subunit POB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1584
Polymers21,9851
Non-polymers1743
Water2,234124
1
A: FACT complex subunit POB3
hetero molecules

A: FACT complex subunit POB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3178
Polymers43,9692
Non-polymers3476
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area2010 Å2
ΔGint-25 kcal/mol
Surface area13430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.268, 68.268, 67.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
DetailsExperimentally unknown. It is predicted to be monomer.

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Components

#1: Protein FACT complex subunit POB3 / Facilitates chromatin transcription complex subunit POB3 / a subunit of the heterodimeric FACT ...Facilitates chromatin transcription complex subunit POB3 / a subunit of the heterodimeric FACT complex (Spt16p-Pob3p)


Mass: 21984.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: POB3, Saccharomyces cerevisiae, YML069W / Plasmid: p15Tv lic / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q04636
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.07 Å3/Da / Density % sol: 40.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Bis-tris, 1.5M (NH4)2SO4., pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 26, 2008 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.7→22.3 Å / Num. all: 20548 / Num. obs: 20548 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 36.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1001 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0054refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→22.3 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.43 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.084 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19211 1034 5.1 %RANDOM
Rwork0.18079 ---
all0.18139 19155 --
obs0.18139 19155 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.465 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20.05 Å20 Å2
2--0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms914 0 10 124 1048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.9241301
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0945122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06123.51954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09215169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8431510
X-RAY DIFFRACTIONr_chiral_restr0.1350.2131
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02757
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.0631.5572
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9392914
X-RAY DIFFRACTIONr_scbond_it3.0723393
X-RAY DIFFRACTIONr_scangle_it4.9884.5382
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.698→1.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 80 -
Rwork0.224 1370 -
obs-1450 96.6 %
Refinement TLS params.Method: refined / Origin x: -0.744 Å / Origin y: 51.428 Å / Origin z: 2.306 Å
111213212223313233
T0.0176 Å2-0.0108 Å20.008 Å2-0.0209 Å2-0.0012 Å2--0.0493 Å2
L1.3526 °20.3693 °20.4274 °2-2.0272 °20.4334 °2--1.553 °2
S-0.0001 Å °0.0922 Å °-0.0367 Å °-0.0635 Å °-0.008 Å °-0.0021 Å °0.0301 Å °0.0533 Å °0.008 Å °

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