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- PDB-2l0d: Solution NMR Structure of putative cell surface protein MA_4588 (... -

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Basic information

Entry
Database: PDB / ID: 2l0d
TitleSolution NMR Structure of putative cell surface protein MA_4588 (272-376 domain) from Methanosarcina acetivorans, Northeast Structural Genomics Consortium Target MvR254A
ComponentsCell surface proteinCell membrane
KeywordsCELL ADHESION / Structural Genomics / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


peptide metabolic process / metallocarboxypeptidase activity / protein processing / calcium ion binding / extracellular space
Similarity search - Function
Domain of unknown function DUF2341 / Protein of unknown function DUF3344 / Domain of unknown function (DUF2341) / Protein of unknown function (DUF3344) / CARDB domain / CARDB / Polycystic kidney disease (PKD) domain profile. / PKD domain / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) ...Domain of unknown function DUF2341 / Protein of unknown function DUF3344 / Domain of unknown function (DUF2341) / Protein of unknown function (DUF3344) / CARDB domain / CARDB / Polycystic kidney disease (PKD) domain profile. / PKD domain / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / PKD domain superfamily / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cell surface protein
Similarity search - Component
Biological speciesMethanosarcina acetivorans (archaea)
MethodSOLUTION NMR / molecular dynamics, simulated annealing
Model detailslowest energy, model 1
AuthorsCort, J.R. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Ramelot, T.A. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR Structure of putative cell surface protein MA_4588 (272-376 domain) from Methanosarcina acetivorans, Northeast Structural Genomics Consortium Target MvR254A
Authors: Cort, J. / Lee, D. / Ciccosanti, C. / Janjua, H. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Kennedy, M.A.
History
DepositionJun 30, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 5, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell surface protein


Theoretical massNumber of molelcules
Total (without water)12,2991
Polymers12,2991
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Cell surface protein / Cell membrane


Mass: 12299.312 Da / Num. of mol.: 1 / Fragment: sequence database residues 272-376
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina acetivorans (archaea) / Gene: MA_4588 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8THC9

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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 HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D 1H-13C arom NOESY
1713D 1H-13C aliph NOESY
1813D 1H-15N NOESY
1924D 1H-13C-13C-1H HMQC-NOESY-HMQC
11013D HBHA(CO)NH
11113D (H)CCH-TOCSY
11213D C(CO)NH
11332D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
21.1 mM [U-100% 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3, 100% D2O100% D2O
31.1 mM [5% biosynthetically-directed 13C; U-100% 15N] MvR254A, 100 mM NaCl, 20 mM MES, 5 mM CaCl2, 0.05 % NaN3, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMMvR254A-1[U-100% 13C; U-100% 15N]1
100 mMNaCl-21
20 mMMES-31
5 mMCaCl2-41
0.05 %NaN3-51
1.1 mMMvR254A-6[U-100% 13C; U-100% 15N]2
100 mMNaCl-72
20 mMMES-82
5 mMCaCl2-92
0.05 %NaN3-102
1.1 mMMvR254A-11[5% biosynthetically-directed 13C; U-100% 15N]3
100 mMNaCl-123
20 mMMES-133
5 mMCaCl2-143
0.05 %NaN3-153
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CNSBrunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNSBrunger, Adams, Clore, Gros, Nilges and Readgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichrefinement
CYANA3Guntert, Mumenthaler and Wuthrichgeometry optimization
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
XEASYBartels et al.data analysis
XEASYBartels et al.peak picking
XEASYBartels et al.chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
SparkyGoddarddata analysis
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
REDCATValafar, Prestegardgeometry optimization
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: molecular dynamics, simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 40 / Conformers submitted total number: 20

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