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- PDB-2ksv: The NMR structure of protein-glutaminase from Chryseobacterium pr... -

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Basic information

Entry
Database: PDB / ID: 2ksv
TitleThe NMR structure of protein-glutaminase from Chryseobacterium proteolyticum
ComponentsProtein-glutaminase
KeywordsHYDROLASE
Function / homologyProtein glutaminase / Glutaminase / C8orf32 fold - #30 / C8orf32 fold / Roll / Alpha Beta / Protein-glutaminase
Function and homology information
Biological speciesChryseobacterium proteolyticum (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsKumeta, H. / Miwa, N. / Ogura, K. / Kai, Y. / Mizukoshi, T. / Shimba, N. / Suzuki, E. / Inagaki, F.
CitationJournal: J.Biomol.Nmr / Year: 2010
Title: The NMR structure of protein-glutaminase from Chryseobacterium proteolyticum.
Authors: Kumeta, H. / Miwa, N. / Ogura, K. / Kai, Y. / Mizukoshi, T. / Shimba, N. / Suzuki, E. / Inagaki, F.
History
DepositionJan 14, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.3Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-glutaminase


Theoretical massNumber of molelcules
Total (without water)19,8751
Polymers19,8751
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 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein Protein-glutaminase


Mass: 19875.297 Da / Num. of mol.: 1 / Fragment: residues 136-320
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chryseobacterium proteolyticum (bacteria)
Strain: 9670 / Gene: prgA / Production host: Corynebacterium glutamicum (bacteria) / References: UniProt: Q9AQQ8, protein-glutamine glutaminase
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D (H)CCH-TOCSY
1513D HNCO
1613D HN(CO)CA
1713D HNCA
1813D HBHA(CO)NH
1913D HN(CA)HA
11013D CBCA(CO)NH
11113D HN(CA)CB
11213D CCH-TOCSY
11313D 1H-13C NOESY
11412D (HB)CB(CGCD)HD
11512D (HB)CB(CGCDCE)HE

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Sample preparation

DetailsContents: 1.15mM [U-13C; U-15N] protein glutaminase-1, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
SampleConc.: 1.15 mM / Component: protein glutaminase-1 / Isotopic labeling: [U-13C; U-15N]
Sample conditionsIonic strength: 20 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.111Goddardchemical shift assignment
Sparky3.111Goddardpeak picking
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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