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- PDB-2jxn: Solution Structure of S. cerevisiae PDCD5-like Protein Ymr074cp -

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Basic information

Entry
Database: PDB / ID: 2jxn
TitleSolution Structure of S. cerevisiae PDCD5-like Protein Ymr074cp
ComponentsUncharacterized protein YMR074C
KeywordsUNKNOWN FUNCTION / Ymr074cp / PDCD5-like protein / Phosphoprotein / Structural Genomics
Function / homology
Function and homology information


DNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
PDCD5, DNA-binding domain / PDCD5-like / PDCD5-like superfamily / Double-stranded DNA-binding domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-MTN / Uncharacterized protein YMR074C
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / distance geometry, molecular dynamics, torsion angle dynamics
AuthorsHong, J. / Zhang, J. / Liu, Z. / Shi, Y. / Wu, J.
CitationJournal: To be Published
Title: Solution Structure and Dynamics of S. cerevisiae PDCD5-like Protein Ymr074cp Determined by Heteronuclear NMR Spectroscopy
Authors: Hong, J. / Zhang, J. / Liu, Z. / Wu, J. / Shi, Y.
History
DepositionNov 23, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
SupersessionDec 9, 2008ID: 2HVU
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 20, 2021Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YMR074C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3873
Polymers13,8581
Non-polymers5292
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 400back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein YMR074C


Mass: 13858.473 Da / Num. of mol.: 1 / Mutation: A7C, A11C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YMR074C / Plasmid: PET-22B(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q04773
#2: Chemical ChemComp-MTN / S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate / MTSL / MTSL


Mass: 264.385 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H18NO3S2

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-15N HSQC
1212D 1H-15N HSQC
1352D 1H-15N IPAP HSQC
1462D 1H-15N IPAP HSQC
1523D CBCA(CO)NH
1623D CBCANH
1723D HNCA
1823D HN(CO)CA
1923D HNCO
11023D HN(CA)CO
11123D C(CO)NH-TOCSY
11223D HBHA(CBCACO)NH
11323D H(CCO)NH-TOCSY
11423D 15N-edited-NOESY-HSQC
11543D (H)CCH-COSY
11643D (H)CCH-TOCSY
11743D 13C-edited-NOESY-HSQC
2184H-D exchange
1195NMR relaxation
1205NMR relaxation
12172D 1H-15N HSQC
12282D 1H-15N HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.2 mM [U-100% 15N] N116 A7C, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % [U-100% 2H] D2O, 90 % H2O, 0.2 mM 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate, 1 mM ascorbate, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-100% 13C; U-100% 15N] N116, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % [U-100% 2H] D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
30.2 mM [U-100% 15N] N116 A7C, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % [U-100% 2H] D2O, 90 % H2O, 0.2 mM 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate, 90% H2O/10% D2O90% H2O/10% D2O
41 mM [U-100% 13C; U-100% 15N] N116, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 100 % [U-100% 2H] D2O, 100% D2O100% D2O
51 mM [U-100% 15N] N116, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % [U-100% 2H] D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
61 mM [U-100% 15N] N116, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % [U-100% 2H] D2O, 90 % H2O, 7 or 8 % polyacrylamide gel, 90% H2O/10% D2O90% H2O/10% D2O
70.2 mM [U-100% 15N] N116 A11C, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % [U-100% 2H] D2O, 90 % H2O, 0.2 mM 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate, 90% H2O/10% D2O90% H2O/10% D2O
80.2 mM [U-100% 15N] N116 A11C, 20 mM sodium phosphate, 50 mM sodium chloride, 1 mM EDTA, 10 % [U-100% 2H] D2O, 90 % H2O, 0.2 mM 1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate, 1 mM ascorbate, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.2 mMN116 A7C[U-100% 15N]1
20 mMsodium phosphate1
50 mMsodium chloride1
1 mMEDTA1
10 %D2O[U-100% 2H]1
90 %H2O1
0.2 mM1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate1
1 mMascorbate1
1 mMN116[U-100% 13C; U-100% 15N]2
20 mMsodium phosphate2
50 mMsodium chloride2
1 mMEDTA2
10 %D2O[U-100% 2H]2
90 %H2O2
0.2 mMN116 A7C[U-100% 15N]3
20 mMsodium phosphate3
50 mMsodium chloride3
1 mMEDTA3
10 %D2O[U-100% 2H]3
90 %H2O3
0.2 mM1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate3
1 mMN116[U-100% 13C; U-100% 15N]4
20 mMsodium phosphate4
50 mMsodium chloride4
1 mMEDTA4
100 %D2O[U-100% 2H]4
1 mMN116[U-100% 15N]5
20 mMsodium phosphate5
50 mMsodium chloride5
1 mMEDTA5
10 %D2O[U-100% 2H]5
90 %H2O5
1 mMN116[U-100% 15N]6
20 mMsodium phosphate6
50 mMsodium chloride6
1 mMEDTA6
10 %D2O[U-100% 2H]6
90 %H2O6
7 %polyacrylamide gel6
0.2 mMN116 A11C[U-100% 15N]7
20 mMsodium phosphate7
50 mMsodium chloride7
1 mMEDTA7
10 %D2O[U-100% 2H]7
90 %H2O7
0.2 mM1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate7
0.2 mMN116 A11C[U-100% 15N]8
20 mMsodium phosphate8
50 mMsodium chloride8
1 mMEDTA8
10 %D2O[U-100% 2H]8
90 %H2O8
0.2 mM1-oxyl-2, 2, 5, 5-tetramethyl-3-pyrroline-3-methylmethanethiosulfonate8
1 mMascorbate8
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
16.0 1 atm298 K
26.0 1 atm295 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Bruker AvanceBrukerAVANCE5002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2Delaglio, F. et al.processing
Sparky3.11Goddard, T.D. et al.peak picking
Sparky3.11Goddard, T.D. et al.chemical shift assignment
TALOSCornilescu, G. et al.data analysis
X-PLOR NIH2.18Schwieters, C.D. et al.structure solution
X-PLOR NIH2.18Schwieters, C.D. et al.refinement
ProcheckLaskowski, R.A. et al.geometry optimization
MOLMOLKoradi, R. et al.data analysis
RefinementMethod: distance geometry, molecular dynamics, torsion angle dynamics
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 400 / Conformers submitted total number: 20

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