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- PDB-2m19: Solution structure of the Haloferax volcanii HVO 2177 protein -

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Basic information

Entry
Database: PDB / ID: 2m19
TitleSolution structure of the Haloferax volcanii HVO 2177 protein
ComponentsMolybdopterin converting factor subunit 1
KeywordsPROTEIN BINDING / ubiquitin-like protein
Function / homology
Function and homology information


MoaD, archaeal-type / : / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Small archaeal modifier protein 3
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodSOLUTION NMR / torsion angle dynamics, simulated annealing
Model detailsclosest to the average, model 7
AuthorsLi, Y. / Maciejewski, M.W. / Martin, J. / Jin, K. / Zhang, Y. / Lu, M. / Maupin-Furlow, J.A. / Hao, B.
CitationJournal: Protein Sci. / Year: 2013
Title: Crystal structure of the ubiquitin-like small archaeal modifier protein 2 from Haloferax volcanii.
Authors: Li, Y. / Maciejewski, M.W. / Martin, J. / Jin, K. / Zhang, Y. / Maupin-Furlow, J.A. / Hao, B.
History
DepositionNov 21, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Oct 2, 2013Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Molybdopterin converting factor subunit 1


Theoretical massNumber of molelcules
Total (without water)11,5411
Polymers11,5411
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Molybdopterin converting factor subunit 1


Mass: 11540.722 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloferax volcanii (archaea) / Strain: DS2 / Gene: HVO_2177 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): DE3 / References: UniProt: D4GVB0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1222D 1H-13C HSQC
1313D HN(CA)CB
1413D HNCO
1513D HCACO
1613D HBHA(CO)NH
1713D C(CO)NH
1813D H(CCO)NH
1923D (H)CCH-TOCSY
11022D 1H-13C HSQC aromatic
11122D 1H-1H NOESY
11213D 1H-15N NOESY
11323D 1H-13C NOESY aliphatic
11423D 1H-13C NOESY aromatic

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] Ubl protein HVO 2177, 90% H2O/10% D2O90% H2O/10% D2O
21 mM [U-99% 13C; U-99% 15N] Ubl protein HVO 2177, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMUbl protein HVO_2177-1[U-99% 13C; U-99% 15N]1
1 mMUbl protein HVO_2177-2[U-99% 13C; U-99% 15N]2
Sample conditionsIonic strength: 0.5 / pH: 7.2 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian VNMRSVarianVNMRS6001
Varian VNMRSVarianVNMRS8002

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Processing

NMR software
NameVersionDeveloperClassification
XEASY1.2Bartels et al.chemical shift assignment
XEASY1.2Bartels et al.peak picking
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
VnmrJ3.1Variancollection
Rowland_NMR_Toolkit3Hoch, Jeffrey C. & Stern, Alan S.processing
CNS1.3Brunger, Adams, Clore, Gros, Nilges and Readrefinement
TALOS+Cornilescu, Delaglio and Baxtorsion angle restraints
TALOS+Shen, Delaglio, Cornilescu, and Baxtorsion angle restraints
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics, simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 3421 / NOE intraresidue total count: 549 / NOE long range total count: 1424 / NOE medium range total count: 640 / NOE sequential total count: 808 / Protein phi angle constraints total count: 82 / Protein psi angle constraints total count: 82
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20

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