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- PDB-3v46: Crystal Structure of Yeast Cdc73 C-Terminal Domain -

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Basic information

Entry
Database: PDB / ID: 3v46
TitleCrystal Structure of Yeast Cdc73 C-Terminal Domain
ComponentsCell division control protein 73
KeywordsTRANSCRIPTION / Ras-like fold / non-GTP binding / Protein Interaction Surface / Transcription Elongation Factor
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 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 / SYNCHROTRON / SAD / Resolution: 1.549 Å
AuthorsAmrich, C.G. / VanDemark, A.P.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Cdc73 subunit of Paf1 complex contains C-terminal Ras-like domain that promotes association of Paf1 complex with chromatin.
Authors: Amrich, C.G. / Davis, C.P. / Rogal, W.P. / Shirra, M.K. / Heroux, A. / Gardner, R.G. / Arndt, K.M. / VanDemark, A.P.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Feb 28, 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


Theoretical massNumber of molelcules
Total (without water)20,0661
Polymers20,0661
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.324, 53.324, 130.223
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-545-

HOH

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Components

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


Mass: 20065.814 Da / Num. of mol.: 1 / Fragment: C-Terminal Domain residues 230-393
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CDC73, YLR418C / Plasmid: pET151 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon Plus / References: UniProt: Q06697
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8
Details: PEG 8000, pH 8.0, VAPOR DIFFUSION, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2510.979
SYNCHROTRONNSLS X2521.1
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 22, 2010
ADSC QUANTUM 3152CCDFeb 22, 2010
Radiation
IDMonochromatorProtocolScattering typeWavelength-ID
1Double silicon(111) crystalSINGLE WAVELENGTHx-ray1
2Double silicon(111) crystalSINGLE WAVELENGTHx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
21.11
ReflectionRedundancy: 12.3 % / Av σ(I) over netI: 58.1 / Number: 230812 / Rmerge(I) obs: 0.064 / Χ2: 0.87 / D res high: 1.78 Å / D res low: 50 Å / Num. obs: 18777 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.835099.910.041.32811.4
3.043.8399.910.0561.48912.3
2.663.0410010.0610.98612.7
2.422.6610010.0780.86912.8
2.242.4210010.0990.78912.9
2.112.2410010.1240.75212.9
22.1110010.1660.6413.1
1.92210010.2480.6313
1.841.9210010.3720.56512.5
1.781.8499.210.5220.5049.4
ReflectionResolution: 1.549→50 Å / Num. all: 28216 / Num. obs: 28111 / % possible obs: 99.3 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.054 / Χ2: 2.038 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.549-1.586.90.3825871.2051,297.8
1.58-1.6170.3325801.191,298.7
1.61-1.6470.26926151.1881,299.2
1.64-1.6770.22925851.2711,299.1
1.67-1.7170.20125941.31,299.3
1.71-1.757.10.17325821.3851,299.3
1.75-1.797.10.1426311.4441,299.3
1.79-1.847.10.12226421.591,299.6
1.84-1.897.10.10125851.7351,299.9
1.89-1.957.20.08826211.8861,299.7
1.95-2.027.20.07726001.9831,299.8
2.02-2.17.30.06826422.1591,2100
2.1-2.27.30.06226152.2531,2100
2.2-2.327.40.05826612.3481,2100
2.32-2.467.40.05625962.4361,2100
2.46-2.657.40.05526532.7461,2100
2.65-2.927.30.05626253.1631,2100
2.92-3.347.20.05226453.3421,2100
3.34-4.216.90.04526413.0721,299.8
4.21-506.80.04325162.8831,293.7

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
18.14837.59103.016SE25.031.18
28.85937.527101.212SE27.740.15
310.91339.783103.949SE21.170.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementResolution: 1.549→37.706 Å / Occupancy max: 1 / Occupancy min: 0.45 / FOM work R set: 0.8784 / SU ML: 0.16 / σ(F): 0.18 / Phase error: 18.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2104 1414 5.03 %
Rwork0.1725 26697 -
obs0.1744 28111 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.378 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 78.97 Å2 / Biso mean: 31.8662 Å2 / Biso min: 11.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.5233 Å2-0 Å20 Å2
2---1.5233 Å2-0 Å2
3---3.0467 Å2
Refinement stepCycle: LAST / Resolution: 1.549→37.706 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1357 0 0 145 1502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071411
X-RAY DIFFRACTIONf_angle_d1.0681917
X-RAY DIFFRACTIONf_chiral_restr0.07200
X-RAY DIFFRACTIONf_plane_restr0.005246
X-RAY DIFFRACTIONf_dihedral_angle_d12.943531
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.549-1.60450.23641380.1542610274899
1.6045-1.66870.18341200.13262624274499
1.6687-1.74470.1991280.127226052733100
1.7447-1.83670.19031360.127526522788100
1.8367-1.95170.1671530.130826022755100
1.9517-2.10240.17891460.140826422788100
2.1024-2.3140.18961490.145926622811100
2.314-2.64870.21021430.167626802823100
2.6487-3.33680.23271660.180527132879100
3.3368-37.71690.21661350.199229073042100

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