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- PDB-4dm4: The conserved domain of yeast Cdc73 -

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Basic information

Entry
Database: PDB / ID: 4dm4
TitleThe conserved domain of yeast Cdc73
ComponentsCell division control protein 73
KeywordsTRANSCRIPTION / Paf1 complex / GTPase-like / transcription elongation / protein binding / nucleus
Function / homology
Function and homology information


positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / negative regulation of DNA recombination / mRNA 3'-end processing / : / RNA polymerase II complex binding / transcription elongation by RNA polymerase I / transcription elongation by RNA polymerase II ...positive regulation of transcription elongation by RNA polymerase I / regulation of transcription-coupled nucleotide-excision repair / RNA polymerase II C-terminal domain phosphoserine binding / Cdc73/Paf1 complex / negative regulation of DNA recombination / mRNA 3'-end processing / : / RNA polymerase II complex binding / transcription elongation by RNA polymerase I / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / euchromatin / chromatin binding / nucleus
Similarity search - Function
RNA polymerase II accessory factor, Cdc73 C-terminal domain / Cdc73/Parafibromin / Cell division control protein 73, C-terminal / Cell division control protein 73, C-terminal domain superfamily / RNA pol II accessory factor, Cdc73 family, C-terminal / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Cell division control protein 73
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.19 Å
AuthorsChen, H. / Shi, N. / Gao, Y. / Li, X. / Niu, L. / Teng, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Crystallographic analysis of the conserved C-terminal domain of transcription factor Cdc73 from Saccharomyces cerevisiae reveals a GTPase-like fold.
Authors: Chen, H. / Shi, N. / Gao, Y. / Li, X. / Teng, M. / Niu, L.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division control protein 73
B: Cell division control protein 73


Theoretical massNumber of molelcules
Total (without water)40,2422
Polymers40,2422
Non-polymers00
Water3,369187
1
A: Cell division control protein 73


Theoretical massNumber of molelcules
Total (without water)20,1211
Polymers20,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cell division control protein 73


Theoretical massNumber of molelcules
Total (without water)20,1211
Polymers20,1211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.938, 96.893, 114.029
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Cell division control protein 73 / RNA polymerase-associated protein CDC73


Mass: 20120.900 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 235-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: CDC73, YLR418C / Production host: Escherichia coli (E. coli) / References: UniProt: Q06697
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 3.12 Å3/Da / Density % sol: 60.59 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.7M Sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.19→73.84 Å / Num. all: 26095 / Num. obs: 26095 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.2→2.24 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.692 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26505 1324 5.1 %RANDOM
Rwork0.22056 ---
obs0.22275 24765 99.64 %-
all-26095 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.347 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2--0.9 Å20 Å2
3----2.03 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 0 187 2775
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222678
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9213649
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2865316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81823.111135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.94815421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8651520
X-RAY DIFFRACTIONr_chiral_restr0.0780.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212090
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_it0.4191.51590
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.822588
X-RAY DIFFRACTIONr_scbond_it1.16931088
X-RAY DIFFRACTIONr_scangle_it1.9154.51061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.193→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 90 -
Rwork0.288 1737 -
obs--95.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2890.1281.22412.2131.10024.03190.16930.0436-0.0117-0.1251-0.0635-0.07570.19020.1034-0.10580.0701-0.01230.03150.06580.01550.059310.980412.062538.4486
22.0687-0.5487-0.90081.1421-0.15535.37310.1555-0.03660.2095-0.06680.01650.1005-0.4966-0.0397-0.1720.09730.03930.00880.06290.04270.125-16.803521.689541.6425
31.3591-0.03490.14030.4507-0.35060.44430.04620.02880.1046-0.03310.00980.0407-0.0629-0.021-0.0560.11630.0050.01380.09030.01840.0863-3.16617.168340.6469
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 160
2X-RAY DIFFRACTION2B4 - 160
3X-RAY DIFFRACTION3A201 - 283
4X-RAY DIFFRACTION3B201 - 304

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