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- PDB-2kpt: Solution NMR structure of the N-terminal domain of cg2496 protein... -

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Basic information

Entry
Database: PDB / ID: 2kpt
TitleSolution NMR structure of the N-terminal domain of cg2496 protein from Corynebacterium glutamicum. Northeast Structural Genomics Consortium Target CgR26A
ComponentsPutative secreted proteinSecretory protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / methods development / alpha/beta / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyDiaminopimelate Epimerase; Chain A, domain 1 - #50 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / :
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Sathyamoorthy, B. / Sukumaran, D.K. / Wang, D. / Buchwald, W.A. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. ...Eletsky, A. / Sathyamoorthy, B. / Sukumaran, D.K. / Wang, D. / Buchwald, W.A. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of the N-terminal domain of cg2496 protein from Corynebacterium glutamicum
Authors: Eletsky, A. / Sathyamoorthy, B. / Sukumaran, D.K. / Wang, D. / Buchwald, W. / Ciccosanti, C. / Janjua, H. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionOct 19, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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: Putative secreted protein


Theoretical massNumber of molelcules
Total (without water)15,8321
Polymers15,8321
Non-polymers00
Water0
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 #1lowest energy

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Components

#1: Protein Putative secreted protein / Secretory protein


Mass: 15831.771 Da / Num. of mol.: 1 / Fragment: sequence database residues 41-180
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg2496 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q6M3G5

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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 aliphatic
1312D 1H-13C CT-HSQC aliphatic
1412D 1H-13C CT-HSQC aromatic
1513D HNCO
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HN(CA)CO
1913D HBHA(CO)NH
11013D (H)CCH-COSY aliphatic
11113D (H)CCH-COSY aromatic
11213D (H)CCH-TOCSY aliphatic
11311D 15N T1
11411D 15N T2
11513D 1H-15N/13C NOESY
11612D (HB)CB(CGCDCE)HE aromatic
11722D 1H-13C CT-HSQC methyl 28ms
11822D 1H-13C CT-HSQC methyl 56ms

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM [U-100% 13C; U-100% 15N] cgr26a, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.9 mM [U-5% 13C; U-100% 15N] cgr26a, 20 mM MES, 200 mM sodium chloride, 5 mM calcium chloride, 50 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMcgr26a-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
200 mMsodium chloride-31
5 mMcalcium chloride-41
50 uMDSS-51
0.02 %sodium azide-61
0.9 mMcgr26a-7[U-100% 13C; U-100% 15N]2
20 mMMES-82
200 mMsodium chloride-92
5 mMcalcium chloride-102
50 uMDSS-112
0.02 %sodium azide-122
0.9 mMcgr26a-13[U-5% 13C; U-100% 15N]3
20 mMMES-143
200 mMsodium chloride-153
5 mMcalcium chloride-163
50 uMDSS-173
0.02 %sodium azide-183
Sample conditionsIonic strength: 225 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameVersionDeveloperClassification
VnmrJ2.1BVariancollection
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
PROSA6.4Guntertprocessing
XEASY1.3.13Bartels et al.data analysis
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichchemical shift assignment
CARA1.8.4Keller and Wuthrichpeak picking
PINE1Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+1.2009.0721.18Shen, Cornilescu, Delaglio and Baxdata analysis
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure validation
PSVS1.4Bhattacharya and Montelionestructure validation
CNS1.2.1Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the ...Details: Structure determination was performed iteratively with CYANA v2.1 using NOE-based constraints and PHI and PSI dihedral angle constraints from TALOS+. The 20 conformers out of 100 with the lowest target function were further refined by simulated annealing in explicit water bath using the program CNS with PARAM19 force field.
NMR constraintsNOE constraints total: 2819 / NOE intraresidue total count: 486 / NOE long range total count: 1072 / NOE medium range total count: 615 / NOE sequential total count: 646 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 73 / Protein psi angle constraints total count: 73
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.05 ° / Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum torsion angle constraint violation: 2.99 ° / Maximum upper distance constraint violation: 0.358 Å
NMR ensemble rmsDistance rms dev: 0.011 Å

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