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- PDB-5ydf: Crystal structure of a disease-related gene, hCDC73(1-100) -

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Basic information

Entry
Database: PDB / ID: 5ydf
TitleCrystal structure of a disease-related gene, hCDC73(1-100)
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 / transcription elongation by RNA polymerase II / regulation of cell growth / positive regulation of transcription elongation by RNA polymerase II / Hedgehog 'on' state / Formation of the beta-catenin:TCF transactivating complex / 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 / SAD / Resolution: 1.399 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 ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Parafibromin
B: Parafibromin


Theoretical massNumber of molelcules
Total (without water)23,3012
Polymers23,3012
Non-polymers00
Water6,269348
1
A: Parafibromin


Theoretical massNumber of molelcules
Total (without water)11,6501
Polymers11,6501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Parafibromin


Theoretical massNumber of molelcules
Total (without water)11,6501
Polymers11,6501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.590, 53.504, 65.734
Angle α, β, γ (deg.)90.00, 95.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 11650.349 Da / Num. of mol.: 2 / Fragment: UNP residues 1-100
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.: 348 / 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: 2.15 Å3/Da / Density % sol: 42.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Tris, magnesium chloride

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL19U110.9785
SYNCHROTRONSSRF BL19U120.9785
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 S 6M1PIXELJan 26, 2016
DECTRIS PILATUS3 S 6M2PIXELApr 2, 2016
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97851
21
ReflectionResolution: 1.4→19.5 Å / Num. obs: 38451 / % possible obs: 98.9 % / Redundancy: 6.6 % / Net I/σ(I): 41.92

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.399→19.489 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1742 1919 4.99 %
Rwork0.1352 --
obs0.1372 38451 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.399→19.489 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1608 0 0 348 1956
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121709
X-RAY DIFFRACTIONf_angle_d1.3612335
X-RAY DIFFRACTIONf_dihedral_angle_d12.904660
X-RAY DIFFRACTIONf_chiral_restr0.063259
X-RAY DIFFRACTIONf_plane_restr0.008299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3989-1.43390.21451460.14662505X-RAY DIFFRACTION95
1.4339-1.47260.18061680.12862564X-RAY DIFFRACTION99
1.4726-1.5160.17451250.11952656X-RAY DIFFRACTION99
1.516-1.56490.17381420.11462576X-RAY DIFFRACTION99
1.5649-1.62080.20081420.12022569X-RAY DIFFRACTION98
1.6208-1.68560.1691300.12622683X-RAY DIFFRACTION100
1.6856-1.76230.19881280.13062603X-RAY DIFFRACTION99
1.7623-1.85510.1771300.13572589X-RAY DIFFRACTION98
1.8551-1.97130.18391180.13862625X-RAY DIFFRACTION99
1.9713-2.12330.18061360.13262632X-RAY DIFFRACTION99
2.1233-2.33670.17241300.13712624X-RAY DIFFRACTION98
2.3367-2.6740.16961400.14772616X-RAY DIFFRACTION99
2.674-3.36620.18671430.14272626X-RAY DIFFRACTION99
3.3662-19.49120.15161410.13222664X-RAY DIFFRACTION98

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