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- PDB-7bmy: p62PH in cesium chloride (0.7 M CsCl in crystallization condition... -

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Basic information

Entry
Database: PDB / ID: 7bmy
Titlep62PH in cesium chloride (0.7 M CsCl in crystallization condition and cryo protectant)
ComponentsRNA polymerase II transcription factor B 73 kDa subunit-like protein
KeywordsTRANSCRIPTION / Cesium / Phasing / Pleckstrin homology domain
Function / homology
Function and homology information


transcription factor TFIIH core complex / nucleotide-excision repair / DNA-templated transcription
Similarity search - Function
TFIIH p62 subunit, N-terminal / TFIIH subunit Tfb1/GTF2H1 / TFIIH p62 subunit, N-terminal domain / BSD domain / BSD domain superfamily / BSD domain / BSD domain profile. / domain in transcription factors and synapse-associated proteins / PH-like domain superfamily
Similarity search - Domain/homology
: / RNA polymerase II transcription factor B 73 kDa subunit-like protein
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsKoelmel, W. / Kuper, J. / Kisker, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)KI 562/11-2 Germany
CitationJournal: Sci Rep / Year: 2021
Title: Cesium based phasing of macromolecules: a general easy to use approach for solving the phase problem.
Authors: Koelmel, W. / Kuper, J. / Kisker, C.
History
DepositionJan 20, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA polymerase II transcription factor B 73 kDa subunit-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,46015
Polymers15,1841
Non-polymers1,27614
Water3,027168
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-288 kcal/mol
Surface area7610 Å2
Unit cell
Length a, b, c (Å)34.426, 106.791, 75.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

CS

21A-402-

HOH

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Components

#1: Protein RNA polymerase II transcription factor B 73 kDa subunit-like protein / p62 pleckstrin homology domain


Mass: 15184.287 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0001260 / Production host: Escherichia coli (E. coli) / References: UniProt: G0RZ08
#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.7 M cesium chloride, 18 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.77114 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77114 Å / Relative weight: 1
ReflectionResolution: 1.8→43.67 Å / Num. obs: 12670 / % possible obs: 94.9 % / Redundancy: 33 % / CC1/2: 0.999 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.026 / Rrim(I) all: 0.152 / Net I/σ(I): 22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.8-1.8421.71.359105444870.8510.2931.3922.765.1
9-43.6731.80.10543581370.9990.0180.10750.899.5

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.8→43.67 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.318 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2145 599 4.7 %RANDOM
Rwork0.1832 ---
obs0.1847 12052 94.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 65.88 Å2 / Biso mean: 19.978 Å2 / Biso min: 8.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2---1.57 Å20 Å2
3---0.72 Å2
Refinement stepCycle: final / Resolution: 1.8→43.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 14 168 1076
Biso mean--40.36 30.33 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02948
X-RAY DIFFRACTIONr_bond_other_d0.0040.02892
X-RAY DIFFRACTIONr_angle_refined_deg2.1081.9921303
X-RAY DIFFRACTIONr_angle_other_deg1.13632093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.595123
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.64124.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10215156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.974156
X-RAY DIFFRACTIONr_chiral_restr0.1330.2149
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211044
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02174
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 25 -
Rwork0.242 592 -
all-617 -
obs--64.27 %

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