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- PDB-7bmu: p62PH in cesium chloride (0.25 M CsCl in protein buffer) -

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Basic information

Entry
Database: PDB / ID: 7bmu
Titlep62PH in cesium chloride (0.25 M CsCl in protein buffer)
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: 1.9 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)15,4636
Polymers15,1841
Non-polymers2785
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area710 Å2
ΔGint-46 kcal/mol
Surface area7750 Å2
Unit cell
Length a, b, c (Å)34.462, 106.517, 75.899
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cs / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.8 M potassium chloride, 17 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 1.9→75.9 Å / Num. obs: 11097 / % possible obs: 97.4 % / Redundancy: 21.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.017 / Rrim(I) all: 0.082 / Net I/σ(I): 28.7 / Num. measured all: 236591
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
1.9-1.9415.20.4597766430.9650.1140.4656.990
9.11-75.919.50.0725931330.9990.0160.07256.299.7

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→53.26 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.902 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2241 595 5.4 %RANDOM
Rwork0.1617 ---
obs0.1652 10482 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.13 Å2 / Biso mean: 28.638 Å2 / Biso min: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.75 Å20 Å20 Å2
2---2.05 Å2-0 Å2
3---1.29 Å2
Refinement stepCycle: final / Resolution: 1.9→53.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 5 154 1053
Biso mean--42.01 38.73 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02942
X-RAY DIFFRACTIONr_bond_other_d0.0020.02882
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.9891293
X-RAY DIFFRACTIONr_angle_other_deg1.03632069
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7095121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.11724.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.19315154
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.393156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02173
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.166 42 -
Rwork0.148 687 -
all-729 -
obs--89.01 %

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