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- PDB-2kw7: Solution NMR Structure of the N-terminal domain of protein PG_036... -

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Basic information

Entry
Database: PDB / ID: 2kw7
TitleSolution NMR Structure of the N-terminal domain of protein PG_0361 from P.gingivalis, Northeast Structural Genomics Consortium Target PgR37A
ComponentsConserved domain proteinProtein domain
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homologyDiaminopimelate Epimerase; Chain A, domain 1 - #50 / TPM domain / TPM domain / Diaminopimelate Epimerase; Chain A, domain 1 / membrane => GO:0016020 / Roll / Alpha Beta / Conserved domain protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsEletsky, A. / Mills, J.L. / Lee, D. / Ciccosanti, C. / Hamilton, K. / 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 protein PG_0361 from P.gingivalis, Northeast Structural Genomics Consortium Target Target PgR37A
Authors: Eletsky, A. / Mills, J.L. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Szyperski, T.
History
DepositionMar 31, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 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_nmr_spectrometer / 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 / _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 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: Conserved domain protein


Theoretical massNumber of molelcules
Total (without water)17,5471
Polymers17,5471
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Conserved domain protein / Protein domain


Mass: 17546.781 Da / Num. of mol.: 1 / Fragment: sequence database residues 35-182
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG_0361 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q7MX54

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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
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1812D 1H-13C HSQC aromatic
1913D (H)CCH-COSY aliphatic
11013D (H)CCH-COSY aromatic
11113D (H)CCH-TOCSY
11222D 1H-13C HSQC
11312D long-range 1H-15N HSQC for histidine
11413D HN(CA)CO

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8 mM [U-100% 13C; U-100% 15N] PgR37A-1, 20 mM MES-2, 100 mM sodium chloride-3, 5 mM calcium chloride-4, 0.02 % sodium azide-5, 50 uM DSS-6, 95% H2O/5% D2O95% H2O/5% D2O
20.8 mM [U-5% 13C; U-100% 15N] PgR37A-7, 20 mM MES-8, 100 mM sodium chloride-9, 5 mM calcium chloride-10, 0.02 % sodium azide-11, 50 uM DSS-12, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.8 mMPgR37A-1[U-100% 13C; U-100% 15N]1
20 mMMES-21
100 mMsodium chloride-31
5 mMcalcium chloride-41
0.02 %sodium azide-51
50 uMDSS-61
0.8 mMPgR37A-7[U-5% 13C; U-100% 15N]2
20 mMMES-82
100 mMsodium chloride-92
5 mMcalcium chloride-102
0.02 %sodium azide-112
50 uMDSS-122
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Varian INOVAVarianINOVA7502

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure solution
AutoStructure2.2.1Huang, Tejero, Powers and Montelionestructure validation
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.3Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
CARA1.8.4Keller and Wuthrichdata analysis
CARA1.8.4Keller and Wuthrichpeak picking
CARA1.8.4Keller and Wuthrichchemical shift assignment
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
VnmrJ2.1BVariancollection
PROSA6.4Guntertprocessing
TALOS+1.2009.0721.18Cornilescu, Delaglio and Baxdata analysis
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 and upper limit constraints relaxed by 5%
NMR constraintsNOE constraints total: 4039 / NOE intraresidue total count: 637 / NOE long range total count: 1331 / NOE medium range total count: 1134 / NOE sequential total count: 937 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 77 / Protein psi angle constraints total count: 77
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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