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- PDB-2m8x: Restrained CS-Rosetta Solution NMR structure of the CARDB domain ... -

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Basic information

Entry
Database: PDB / ID: 2m8x
TitleRestrained CS-Rosetta Solution NMR structure of the CARDB domain of PF1109 from Pyrococcus furiosus. Northeast Structural Genomics Consortium target PfR193A
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / CARDB domain / PFAM 07705 / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / PSI-Biology / Protein Structure Initiative
Function / homologyCARDB domain / CARDB / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / metal ion binding / CARDB domain-containing protein
Function and homology information
Biological speciesPyrococcus furiosus (archaea)
MethodSOLUTION NMR
Model detailslowest energy, model1
AuthorsMao, B. / Tejero, R.T. / Aramini, J.M. / Snyder, D.A. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biomol.Nmr / Year: 2013
Title: PDBStat: a universal restraint converter and restraint analysis software package for protein NMR.
Authors: Tejero, R. / Snyder, D. / Mao, B. / Aramini, J.M. / Montelione, G.T.
History
DepositionMay 29, 2013Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 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:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,8681
Polymers12,8681
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 / 10000structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 12868.411 Da / Num. of mol.: 1 / Fragment: CARDB domain (UNP residues 436-540) / Mutation: N68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: PF1109 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)MGK / References: UniProt: Q8U1U6

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: restrained CS-Rosetta structure refinement
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY aliphatic
1513D 1H-13C NOESY aromatic
1622D 1H-13C HSQC high resolution (L/V methyl stereoassignment)
1713D HNCO
1813D HN(CA)CO
1913D HN(CO)CA
11013D HNCA
11113D CBCA(CO)NH
11213D HN(CA)CB
11313D HBHA(CO)NH
11413D (H)CCH-TOCSY
11513D (H)CCH-COSY
11613D CCH-TOCSY
11713D HNHA
11812D 1H-15N hetNOE
11911D 15N T1 and T2
NMR detailsText: THE FIRST REPRESENTATIVE STRUCTURE IN THE ENSEMBLE IS THE MEDOID STRUCTURE.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.65 mM [U-100% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 10 % D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
20.43 mM [U-5% 13C; U-100% 15N] PfR193A, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 10 mM DTT, 0.02 % sodium azide, 50 uM DSS, 10 % D2O, 90 % H2O, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.65 mMPfR193A-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
10 mMDTT-51
0.02 %sodium azide-61
50 uMDSS-71
10 %D2O-81
90 %H2O-91
0.43 mMPfR193A-10[U-5% 13C; U-100% 15N]2
20 mMMES-112
200 mMsodium chloride-122
5 mMcalcium chloride-132
10 mMDTT-142
0.02 %sodium azide-152
50 uMDSS-162
10 %D2O-172
90 %H2O-182
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospindata analysis
NMRPipe2.3Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.112Goddarddata analysis
Sparky3.112Goddardpeak picking
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionerpf analysis
PSVS1.3Bhattacharya and Montelionestructure quality analysis
MolProbity3.15Richardsonstructure quality analysis
PdbStat5.9Tejero and Montelionepdb coordinate analysis
TALOSplusCornilescu, Delaglio and Baxdihedral angle constraints
Rosetta3Rohl, Strauss, Misura, and Bakerrefinement
RefinementSoftware ordinal: 1
Details: Structures were calculated by Restrained CS-Rosetta method using NOE-based distance and dihedral angle restraints from the original CNS-water refined structure calculations
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 10000 / Conformers submitted total number: 20

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