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- PDB-2kut: Solution Structure of GmR58A from Geobacter metallireducens. Nort... -

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Basic information

Entry
Database: PDB / ID: 2kut
TitleSolution Structure of GmR58A from Geobacter metallireducens. Northeast Structural Genomics Consortium Target GmR58A
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyCARDB domain / CARDB / Papain-like cysteine peptidase superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / CARDB domain lipoprotein, putative
Function and homology information
Biological speciesGeobacter metallireducens (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model 1
AuthorsLee, H. / Wang, H. / Buchwald, W.A. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Lee, H. / Wang, H. / Buchwald, W.A. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Prestegard, J.H. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution Structure of GmR58A
Authors: Lee, H. / Montelione, G.T. / Prestegard, J.H.
History
DepositionFeb 28, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: pdbx_database_status / pdbx_nmr_sample_details ...pdbx_database_status / pdbx_nmr_sample_details / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents ..._pdbx_database_status.status_code_cs / _pdbx_nmr_sample_details.contents / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 8, 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)13,1341
Polymers13,1341
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Uncharacterized protein


Mass: 13133.794 Da / Num. of mol.: 1 / Fragment: sequence database residues 470-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter metallireducens (bacteria) / Strain: GS-15 / ATCC 53774 / DSM 7210 / Gene: Gmet_1998 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q39U47

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
1112NH J-modulation
1123NH J-modulation
1134NH J-modulation

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Sample preparation

Details
Solution-IDContentsSolvent system
10.77 mM [U-100% 13C; U-100% 15N] GmR58A-1, 2 % sodium azide-2, 10 mM DTT-3, 5 mM CaCl-4, 200 mM sodium chloride-5, 20 mM MES-6, 95% H2O/5% D2O95% H2O/5% D2O
20.65 mM [U-100% 13C; U-100% 15N] GmR58A-7, 2 % sodium azide-8, 10 mM DTT-9, 5 mM CaCl-10, 200 mM sodium chloride-11, 20 mM MES-12, 4.2 % C12E5-13, 95% H2O/5% D2O95% H2O/5% D2O
30.65 mM [U-100% 13C; U-100% 15N] GmR58A-14, 2 % sodium azide-15, 10 mM DTT-16, 5 mM CaCl-17, 200 mM sodium chloride-18, 20 mM MES-19, 7 % negatively charged compressed polyacrylamide gel-20, 95% H2O/5% D2O95% H2O/5% D2O
40.65 mM [U-100% 13C; U-100% 15N] GmR58A-21, 2 % sodium azide-22, 10 mM DTT-23, 5 mM CaCl-24, 200 mM sodium chloride-25, 20 mM MES-26, 5 % Neutral stretched polyacrylamide gel-27, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.77 mMGmR58A-1[U-100% 13C; U-100% 15N]1
2 %sodium azide-21
10 mMDTT-31
5 mMCaCl-41
200 mMsodium chloride-51
20 mMMES-61
0.65 mMGmR58A-7[U-100% 13C; U-100% 15N]2
2 %sodium azide-82
10 mMDTT-92
5 mMCaCl-102
200 mMsodium chloride-112
20 mMMES-122
4.2 %C12E5-132
0.65 mMGmR58A-14[U-100% 13C; U-100% 15N]3
2 %sodium azide-153
10 mMDTT-163
5 mMCaCl-173
200 mMsodium chloride-183
20 mMMES-193
7 %negatively charged compressed polyacrylamide gel-203
0.65 mMGmR58A-21[U-100% 13C; U-100% 15N]4
2 %sodium azide-224
10 mMDTT-234
5 mMCaCl-244
200 mMsodium chloride-254
20 mMMES-264
5 %Neutral stretched polyacrylamide gel-274
Sample conditionsIonic strength: 200 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
X-PLOR NIH2.18Schwieters, Kuszewski, Tjandra and Clorerefinement
Sparky3.115Goddardchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVSBhattacharya and Montelionedata analysis
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxdata analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 10

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