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- PDB-2kzw: Solution NMR Structure of Q8PSA4 from Methanosarcina mazei, North... -

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Basic information

Entry
Database: PDB / ID: 2kzw
TitleSolution NMR Structure of Q8PSA4 from Methanosarcina mazei, Northeast Structural Genomics Consortium Target MaR143A
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Parallel beta-helix repeat-2 / Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / Parallel beta-helix repeat / Parallel beta-helix repeats / PKD domain superfamily / PKD/Chitinase domain ...Parallel beta-helix repeat-2 / Periplasmic copper-binding protein NosD, beta helix domain / Periplasmic copper-binding protein (NosD) / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / Parallel beta-helix repeat / Parallel beta-helix repeats / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Pectin lyase fold / Pectin lyase fold/virulence factor / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Eletsky, A. / Lee, H. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. ...Mills, J.L. / Eletsky, A. / Lee, H. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target MaR143A
Authors: Mills, J.L. / Eletsky, A. / Lee, H. / Lee, D. / Ciccosanti, C. / Hamilton, K. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T.
History
DepositionJun 25, 2010Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 7, 2012Group: Database references / Structure summary
Revision 1.3Feb 5, 2020Group: Data collection / Database references / Other
Category: pdbx_database_status / pdbx_nmr_software ...pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / 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 1.4Jun 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 1.5May 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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,2711
Polymers16,2711
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Uncharacterized protein


Mass: 16271.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: MM_3178 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: Q8PSA4

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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 HBHA(CO)NH
1713D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY
1832D 1H-15N HSQC
1922D 1H-13C HSQC
11013D (H)CCH-TOCSY
11113D (H)CCH-COSY
1121HB(CBCGCDCE)HE

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Sample preparation

Details
Solution-IDContentsSolvent system
10.55 mM [U-100% 13C; U-100% 15N] MaR143A, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
20.55 mM [U-5% 13C; U-100% 15N] MaR143A, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 95% H2O/5% D2O95% H2O/5% D2O
30.55 mM [U-5% 13C; U-100% 15N] MaR143A, 100 mM sodium chloride, 5 mM DTT, 0.02 % sodium azide, 10 mM TRIS, 13 mg/mL Pf1 phage, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.55 mMMaR143A-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
5 mMDTT-31
0.02 %sodium azide-41
10 mMTRIS-51
0.55 mMMaR143A-6[U-5% 13C; U-100% 15N]2
100 mMsodium chloride-72
5 mMDTT-82
0.02 %sodium azide-92
10 mMTRIS-102
0.55 mMMaR143A-11[U-5% 13C; U-100% 15N]3
100 mMsodium chloride-123
5 mMDTT-133
0.02 %sodium azide-143
10 mMTRIS-153
13 mg/mLPf1 phage-163
Sample conditionspH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Varian INOVAVarianINOVA7502
Varian INOVAVarianINOVA6003

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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 Wuthrichtructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis,refinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PROSAGuntertprocessing
CARA1.8Keller et al.data analysis,peak picking,chemical shift assignment
TopSpinBruker Biospincollection
VnmrJVariancollection
PINEBahrami, Markley, Assadi, and Eghbalniachemical shift assignment
TALOS+Shen, Cornilescu, Delaglio and Baxgeometry optimization
PALESPALES (Zweckstetter, Bax)geometry optimization
RefinementMethod: simulated annealing, molecular dynamics / Software ordinal: 1
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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