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- PDB-2k52: Structure of uncharacterized protein MJ1198 from Methanocaldococc... -

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Basic information

Entry
Database: PDB / ID: 2k52
TitleStructure of uncharacterized protein MJ1198 from Methanocaldococcus jannaschii. Northeast Structural Genomics Target MjR117B
ComponentsUncharacterized protein MJ1198
Keywordsstructural genomics / unknown function / Uncharacterized protein / Metal-binding / Zinc / Zinc-finger / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


heat shock protein binding / unfolded protein binding / nucleic acid binding / metal ion binding
Similarity search - Function
Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / DDH domain / DHH family / Heat shock protein DnaJ, cysteine-rich domain superfamily / DHH phosphoesterase superfamily / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain ...Heat shock protein DnaJ, cysteine-rich domain / Zinc finger CR-type profile. / DDH domain / DHH family / Heat shock protein DnaJ, cysteine-rich domain superfamily / DHH phosphoesterase superfamily / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding proteins / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Nucleic acid-binding, OB-fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein MJ1198
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsRossi, P. / Maglaqui, M. / Foote, E.L. / Hamilton, K. / Ciccosanti, C. / Xiao, R. / Nair, R. / Swapna, G. / Everett, J.K. / Acton, T.B. ...Rossi, P. / Maglaqui, M. / Foote, E.L. / Hamilton, K. / Ciccosanti, C. / Xiao, R. / Nair, R. / Swapna, G. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Structure of uncharacterized protein MJ1198 from Methanocaldococcus jannaschii. Northeast Structural Genomics Target MjR117B
Authors: Rossi, P. / Xiao, R. / Acton, T.B. / Montelione, G.T.
History
DepositionJun 24, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein MJ1198


Theoretical massNumber of molelcules
Total (without water)9,5031
Polymers9,5031
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1

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Components

#1: Protein Uncharacterized protein MJ1198


Mass: 9502.940 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Genus: Methanococcus / Species: jannaschii
Description: Expression media: MJ9 100%N15 5%C13 MJ9 100%N15 100%C13
Gene: MJ1198 / Plasmid: pET 21-23C / Species (production host): coli / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q58598

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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 CBCA(CO)NH
1413D HNCO
1513D HN(CO)CA
1613D HBHA(CO)NH
1713D HN(CA)CB
1813D HN(CA)CO
1913D (H)CCH-TOCSY
11013D (H)CCH-COSY
11113D CCH- TOCSY
11213D SIM 13C
113115N NOESY
11413D ARO 13C NOESY
11512D 1H-13C HSQC STEREO
11612D HETNOE
1171PSEUDO 2D N15 T1
1181PSEUDO 2D N15 T2 (CPMG)
11912D 1H-13C HSQC CT ARO
NMR detailsText: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2 (MS) = 792.1/78.18, TAUC = 9.7(NS) CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR ...Text: MONOMER BY GEL FILTRATION CHROMATOGRAPHY/LIGHT SCATTERING AND BY NMR. T1/T2 (MS) = 792.1/78.18, TAUC = 9.7(NS) CONSISTENT WITH MOLECULAR WEIGHT. STRUCTURE DETERMINED BY TRIPLE RESONANCE NMR SPECTROSCOPY. NOESY ASSIGNMENTS BY CYANA2.1. 20 OF 100 STRUCTURES LOWEST TARGET FUNCTION SELECTED WITH CYANA2.1. SELECTED MODELS ARE FURTHER REFINED USING CNS IN EXPLICIT WATER SHELL (NILGES PROTOCOL WITH PARAM19). ASSIGNMENT STATS AROMATIC (SC) 92.6%, VL METHYL STEREOSPECIFIC 100%, UNAMBIGUOS SIDECHAIN NH2 100%. STRUCTURE BASED ON 1088 NOE, 166 DIHE. MAX NOE VIOLATION: 0.25 A (1MODEL); MAX DIHE VIOLATION: 3.2 DEG. 2 TOTAL CLOSE CONTACTS PER 20 MODELS. STRUCTURE QUALITY FACTOR > 1.8. SECONDARY STRUCTURE - BETA STRANDS: (8-17, 20-26, 29- 33, 51-60, 65-70). RMSD 0.4 BACKBONE, 0.8 ALL HEAVY ATOMS. MOLPROBITY CLASH: 16.80/-1.36 (RAW/Z). RPF SCORES ALL ASSIGNED PRECISION: 0.89, F-MEASURE: 0.93, DP-SCORE: 0.83.

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Sample preparation

DetailsContents: 1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; ...Contents: 1.682 MM [U-100% 13C 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O; 1.226 MM [5% 13C; U- 100% 15N] MJR117B, 20 MM AMMONIUM ACETATE, 100 MM SODIUM CHLORIDE, 0.02 MM SODIUM AZIDE, 10 MM DTT, 50 UM DSS, 5 MM CALCIUM CHLORIDE, 1X PROTEASE INHIBITOR, 90% H2O/ 10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.682 mMMjR117B[U-100% 13C; U-100% 15N]1
20 mMammonium acetate1
100 mMsodium chloride1
0.02 mMsodium azide1
10 mMDTT1
50 uMDSS1
5 mMcalcium chloride1
1 mMprotease inhibitor1
1.226 mMMjR117B[5% 13C; U-100% 15N]2
20 mMammonium acetate2
100 mMsodium chloride2
0.02 mMsodium azide2
10 mMDTT2
50 uMDSS2
5 mMcalcium chloride2
1 mMprotease inhibitor2
Sample conditionsIonic strength: 0.1 / pH: 4.5 / Pressure: AMBIENT / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE6001
Bruker AVANCEBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1BRUNGER, ADAMS, CLORE, GROS, NILGESrefinement
CYANA2.1structure solution
NMRPipestructure solution
AutoAssignstructure solution
Sparky3.113structure solution
TopSpin2.1structure solution
RPF(AUTOSTRUCTURE)2.2.1structure solution
PSVS1.3structure solution
MOLMOLstructure solution
PROCHECKstructure solution
MolProbitystructure solution
TALOSstructure solution
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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