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- PDB-7bmz: p62PH in potassium chloride -

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Basic information

Entry
Database: PDB / ID: 7bmz
Titlep62PH in potassium chloride
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: 2.5 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)15,2593
Polymers15,1841
Non-polymers752
Water91951
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-8 kcal/mol
Surface area7670 Å2
Unit cell
Length a, b, c (Å)34.736, 106.174, 76.209
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-336-

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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 0.9 M potassium chloride, 19 % (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7712 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.5→43.56 Å / Num. obs: 5119 / % possible obs: 99.1 % / Redundancy: 12.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.041 / Rrim(I) all: 0.149 / Net I/σ(I): 14.4
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
2.5-2.66.91.17636045210.6330.4731.2721.693
9.02-43.5611.40.07515341350.9970.0230.07932.899.5

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Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
REFMACphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→43.56 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.892 / SU B: 11.352 / SU ML: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.518 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2657 262 5.1 %RANDOM
Rwork0.2024 ---
obs0.2057 4844 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.89 Å2 / Biso mean: 41.74 Å2 / Biso min: 22.51 Å2
Baniso -1Baniso -2Baniso -3
1--1.68 Å2-0 Å2-0 Å2
2--2.03 Å2-0 Å2
3----0.36 Å2
Refinement stepCycle: final / Resolution: 2.5→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 2 51 947
Biso mean--56.67 35.3 -
Num. residues----115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02945
X-RAY DIFFRACTIONr_bond_other_d0.0040.02891
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.991296
X-RAY DIFFRACTIONr_angle_other_deg0.96432090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1575121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.16324.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.84915157
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.647156
X-RAY DIFFRACTIONr_chiral_restr0.0910.2147
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0221037
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02173
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 18 -
Rwork0.227 309 -
all-327 -
obs--88.38 %

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