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- PDB-4pq0: Crystal structure of POB3 middle domain at 1.65A -

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Basic information

Entry
Database: PDB / ID: 4pq0
TitleCrystal structure of POB3 middle domain at 1.65A
ComponentsFACT complex subunit POB3
KeywordsREPLICATION / TRANSCRIPTION / double pleckstrin homology (PH)architecture
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 / nucleosome binding / DNA-templated DNA replication ...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 / nucleosome binding / DNA-templated DNA replication / chromatin organization / histone binding / DNA repair / chromatin / DNA binding
Similarity search - Function
PH-domain like - #150 / : / 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 ...PH-domain like - #150 / : / 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
MALONIC ACID / FACT complex subunit POB3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLiu, H.
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of POB3 middle domain at 1.65A
Authors: Liu, H.
History
DepositionFeb 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Non-polymer description
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: FACT complex subunit POB3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1332
Polymers28,0291
Non-polymers1041
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.080, 59.150, 144.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-721-

HOH

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Components

#1: Protein FACT complex subunit POB3 / Facilitates chromatin transcription complex subunit POB3


Mass: 28028.754 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 232-473
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: POB3, YML069W / Production host: Escherichia coli (E. coli) / References: UniProt: Q04636
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1M Sodium malonate pH 7.0, 0.1M Ammonium acetate, 20% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→72.46 Å / Num. all: 33101 / Num. obs: 31370 / Observed criterion σ(F): 0 / Observed criterion σ(I): 3

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.8.0049refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→28.98 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.11 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24813 1670 5.1 %RANDOM
Rwork0.21407 ---
obs0.2157 31370 99.63 %-
all-33101 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å2-0 Å20 Å2
2--0.54 Å2-0 Å2
3----0.78 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 7 148 1978
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191866
X-RAY DIFFRACTIONr_bond_other_d0.0060.021733
X-RAY DIFFRACTIONr_angle_refined_deg1.4271.9692530
X-RAY DIFFRACTIONr_angle_other_deg0.75333970
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.395231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63824.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49615305
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7631510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2289
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212115
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
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_it1.5262.691930
X-RAY DIFFRACTIONr_mcbond_other1.5252.688929
X-RAY DIFFRACTIONr_mcangle_it2.4394.0271159
X-RAY DIFFRACTIONr_mcangle_other1.914.0321160
X-RAY DIFFRACTIONr_scbond_it1.6552.699936
X-RAY DIFFRACTIONr_scbond_other1.1522.651934
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.933.9441371
X-RAY DIFFRACTIONr_long_range_B_refined3.61721.1432093
X-RAY DIFFRACTIONr_long_range_B_other3.43321.0242038
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 120 -
Rwork0.27 2254 -
obs--99.92 %

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