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- PDB-2kzx: Solution NMR Structure of A3DHT5 from Clostridium thermocellum, N... -

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Basic information

Entry
Database: PDB / ID: 2kzx
TitleSolution NMR Structure of A3DHT5 from Clostridium thermocellum, Northeast Structural Genomics Consortium Target CmR116
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


FMN binding / membrane
Similarity search - Function
Sufe protein. Chain: A - #20 / Sufe protein. Chain: A / FMN-binding / FMN-binding domain / FMN_bind / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FMN-binding domain protein
Similarity search - Component
Biological speciesClostridium thermocellum (bacteria)
MethodSOLUTION NMR / simulated annealing, molecular dynamics
Model detailslowest energy, model 1
AuthorsMills, J.L. / Eletsky, A. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. ...Mills, J.L. / Eletsky, A. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, R. / Rost, B. / 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 CmR116
Authors: Mills, J.L. / Eletsky, A. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / ...Authors: Mills, J.L. / Eletsky, A. / Lee, H. / Janjua, H. / Ciccosanti, C. / Wang, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Prestegard, J.H. / Montelione, G.T. / Szyperski, T. / Northeast Structural Genomics Consortium (NESG)
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 1.2Feb 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 1.3Jun 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: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)14,8491
Polymers14,8491
Non-polymers00
Water00
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: 14849.235 Da / Num. of mol.: 1 / Fragment: sequence database residues 38-159
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium thermocellum (bacteria) / Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2312 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pMgK / References: UniProt: A3DHT5

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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
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D HN(CA)CO
11132D 1H-15N HSQC
11222D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.97 mM [U-100% 13C; U-100% 15N] CmR116, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
21.0 mM [U-5% 13C; U-100% 15N] CmR116, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM MES, 90% H2O/10% D2O90% H2O/10% D2O
31.0 mM [U-5% 13C; U-100% 15N] CmR116, 0.02 % sodium azide, 10 mM DTT, 5 mM calcium chloride, 100 mM sodium chloride, 20 mM MES, 4 % PEG, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.97 mMCmR116-1[U-100% 13C; U-100% 15N]1
0.02 %sodium azide-21
10 mMDTT-31
5 mMcalcium chloride-41
100 mMsodium chloride-51
20 mMMES-61
1.0 mMCmR116-7[U-5% 13C; U-100% 15N]2
0.02 %sodium azide-82
10 mMDTT-92
5 mMcalcium chloride-102
100 mMsodium chloride-112
20 mMMES-122
1.0 mMCmR116-13[U-5% 13C; U-100% 15N]3
0.02 %sodium azide-143
10 mMDTT-153
5 mMcalcium chloride-163
100 mMsodium chloride-173
20 mMMES-183
4 %PEG-193
Sample conditionspH: 6.5 / 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 Wuthrichstructure solution
AutoStructure2.1Huang, Tejero, Powers and Montelionedata analysis
AutoStructure2.1Huang, Tejero, Powers and Montelionerefinement
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionedata analysis
AutoAssign2.1Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PROSAGuntertprocessing
CARA1.8Keller et al.data analysis
CARA1.8Keller et al.peak picking
CARA1.8Keller et al.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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