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- PDB-5yde: Crystal structure of a disease-related gene, hCDC73(1-111) -

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Basic information

Entry
Database: PDB / ID: 5yde
TitleCrystal structure of a disease-related gene, hCDC73(1-111)
ComponentsParafibromin
KeywordsTRANSCRIPTION / Tumor suppressor / cancer
Function / homology
Function and homology information


positive regulation of mRNA 3'-end processing / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / mRNA 3'-end processing / : / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / RNA polymerase II complex binding ...positive regulation of mRNA 3'-end processing / Cdc73/Paf1 complex / endodermal cell fate commitment / negative regulation of myeloid cell differentiation / positive regulation of cell cycle G1/S phase transition / mRNA 3'-end processing / : / negative regulation of G1/S transition of mitotic cell cycle / stem cell population maintenance / RNA polymerase II complex binding / positive regulation of Wnt signaling pathway / RNA Polymerase II Transcription Elongation / Formation of RNA Pol II elongation complex / negative regulation of fibroblast proliferation / RNA Polymerase II Pre-transcription Events / regulation of cell growth / transcription elongation by RNA polymerase II / positive regulation of transcription elongation by RNA polymerase II / Formation of the beta-catenin:TCF transactivating complex / Hedgehog 'on' state / protein destabilization / Wnt signaling pathway / negative regulation of epithelial cell proliferation / E3 ubiquitin ligases ubiquitinate target proteins / cellular response to lipopolysaccharide / chromosome, telomeric region / cell cycle / negative regulation of cell population proliferation / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol
Similarity search - Function
Paf1 complex subunit Cdc73, N-terminal domain / Paf1 complex subunit CDC73 N-terminal / 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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.023 Å
AuthorsSun, W. / Kuang, X.L. / Liu, Y.P. / Tian, L.F. / Yan, X.X. / Xu, W.Q.
CitationJournal: Sci Rep / Year: 2017
Title: Crystal structure of the N-terminal domain of human CDC73 and its implications for the hyperparathyroidism-jaw tumor (HPT-JT) syndrome
Authors: Sun, W. / Kuang, X.L. / Liu, Y.P. / Tian, L.F. / Yan, X.X. / Xu, W.
History
DepositionSep 13, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parafibromin


Theoretical massNumber of molelcules
Total (without water)12,7561
Polymers12,7561
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6710 Å2
Unit cell
Length a, b, c (Å)38.091, 43.683, 67.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Parafibromin / Cell division cycle protein 73 homolog / Hyperparathyroidism 2 protein


Mass: 12756.470 Da / Num. of mol.: 1 / Fragment: UNP residues 1-111
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDC73, C1orf28, HRPT2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6P1J9
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.21 Å3/Da / Density % sol: 44.22 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.02→19.4 Å / Num. obs: 109711 / % possible obs: 99 % / Redundancy: 6.3 % / Net I/σ(I): 38.61

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.023→19.399 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 11.1
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.1393 5518 5.03 %
Rwork0.1194 --
obs0.1204 109711 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.023→19.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms893 0 0 284 1177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011978
X-RAY DIFFRACTIONf_angle_d1.5051338
X-RAY DIFFRACTIONf_dihedral_angle_d12.012385
X-RAY DIFFRACTIONf_chiral_restr0.109149
X-RAY DIFFRACTIONf_plane_restr0.01172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0233-1.03490.2092000.17163316X-RAY DIFFRACTION95
1.0349-1.04710.16271500.16493460X-RAY DIFFRACTION100
1.0471-1.05990.17271850.14253479X-RAY DIFFRACTION100
1.0599-1.07330.15081700.12673542X-RAY DIFFRACTION100
1.0733-1.08740.1362070.12353397X-RAY DIFFRACTION100
1.0874-1.10230.14232000.11943422X-RAY DIFFRACTION100
1.1023-1.11810.13641780.11973559X-RAY DIFFRACTION100
1.1181-1.13480.13881910.11643444X-RAY DIFFRACTION100
1.1348-1.15250.162200.11853455X-RAY DIFFRACTION100
1.1525-1.17140.11481890.11043450X-RAY DIFFRACTION100
1.1714-1.19160.12061540.10493524X-RAY DIFFRACTION100
1.1916-1.21320.13022030.10013476X-RAY DIFFRACTION100
1.2132-1.23660.13971820.09923484X-RAY DIFFRACTION100
1.2366-1.26180.12731710.10323458X-RAY DIFFRACTION100
1.2618-1.28920.10112260.0993493X-RAY DIFFRACTION100
1.2892-1.31920.13881690.09973482X-RAY DIFFRACTION100
1.3192-1.35220.12071500.10343511X-RAY DIFFRACTION100
1.3522-1.38880.12482120.10223414X-RAY DIFFRACTION100
1.3888-1.42960.13221630.10193479X-RAY DIFFRACTION100
1.4296-1.47570.12031960.09443497X-RAY DIFFRACTION100
1.4757-1.52850.11341820.09633490X-RAY DIFFRACTION100
1.5285-1.58960.1272010.09723482X-RAY DIFFRACTION100
1.5896-1.66190.14831450.10293489X-RAY DIFFRACTION100
1.6619-1.74950.13191770.10763518X-RAY DIFFRACTION100
1.7495-1.8590.12641880.1123450X-RAY DIFFRACTION100
1.859-2.00240.13931720.11173520X-RAY DIFFRACTION100
2.0024-2.20370.13751850.11353457X-RAY DIFFRACTION100
2.2037-2.5220.12961710.12013509X-RAY DIFFRACTION100
2.522-3.17520.1411890.13183478X-RAY DIFFRACTION100
3.1752-19.4030.17061920.15753458X-RAY DIFFRACTION100

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