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- PDB-2kpi: Solution NMR structure of Streptomyces coelicolor SCO3027 modeled... -

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Basic information

Entry
Database: PDB / ID: 2kpi
TitleSolution NMR structure of Streptomyces coelicolor SCO3027 modeled with Zn+2 bound, Northeast Structural Genomics Consortium Target RR58
ComponentsUncharacterized protein SCO3027
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / zinc finger / PSI-2 / NESG / all beta / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyTrm112-like / Trm112p-like protein / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / Single Sheet / Mainly Beta / cytosol / UPF0434 protein SCO3027
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsC4 zinc-binding protein
AuthorsRamelot, T.A. / Cort, J.R. / Garcia, M. / Yee, A. / Arrowmith, C.H. / Montelione, G.T. / Kennedy, M.A. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Solution NMR structure of Streptomyces coelicolor SCO3027 modeled with Zn+2 bound, Northeast Structural Genomics Consortium Target RR58
Authors: Ramelot, T.A. / Cort, J.R. / Garcia, M. / Yee, A. / Arrowmith, C.H. / Montelione, G.T. / Kennedy, M.A.
History
DepositionOct 15, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0Feb 2, 2010Provider: 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
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein SCO3027
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1142
Polymers6,0491
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 30structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein Uncharacterized protein SCO3027


Mass: 6048.983 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: SCD84.08c, SCE34.08c, SCO3027 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) gold pMGK / References: UniProt: Q9KZL7
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: C4 zinc-binding protein
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D 1H-15N NOESY
1413D 1H-13C NOESY aliph
1513D HNCO
1613D CBCA(CO)NH
1713D HN(CA)CB
1813D HBHA(CO)NH
1913D (H)CCH-TOCSY
11013D (H)CCH-TOCSY
11124D (H)CCH NOESY
11213D C(CO)NH
11313D H(CCO)NH
11432D 1H-13C HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
110 mM Tris, 300 mM sodium chloride, 10 mM zinc chloride, 10 mM DTT, 0.01 % sodium azide, 0.9 mM [U-100% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
210 mM Tris, 300 mM sodium chloride, 10 mM zinc chloride, 10 mM DTT, 0.01 % sodium azide, 0.9 mM [U-100% 13C; U-100% 15N] protein, 100% D2O100% D2O
310 mM Tris, 300 mM sodium chloride, 10 mM zinc chloride, 10 mM DTT, 0.01 % sodium azide, 0.9 mM [U-7% 13C; U-100% 15N] protein, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
10 mMTris1
300 mMsodium chloride1
10 mMzinc chloride1
10 mMDTT1
0.01 %sodium azide1
0.9 mMprotein[U-100% 13C; U-100% 15N]1
10 mMTris2
300 mMsodium chloride2
10 mMzinc chloride2
10 mMDTT2
0.01 %sodium azide2
0.9 mMprotein[U-100% 13C; U-100% 15N]2
10 mMTris3
300 mMsodium chloride3
10 mMzinc chloride3
10 mMDTT3
0.01 %sodium azide3
0.9 mMprotein[U-7% 13C; U-100% 15N]3
Sample conditionsIonic strength: 200 / pH: 7.0 / Pressure: ambient / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Bruker AvanceIIIBrukerAVANCE III8502
Varian INOVAVarianINOVA5003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2008Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
VNMR6.1CVariancollection
TopSpin2.1.4Bruker Biospincollection
AutoStructure2.2.1Huang, Tejero, Powers and Montelionedata analysis
X-PLOR NIH2.2Schwieters, Kuszewski, Tjandra and Clorestructure solution
Sparky3.113Goddarddata analysis
PSVS1.3Bhattacharya and Montelionestructure validation
AutoAssign2.3.0Zimmerman, Moseley, Kulikowski and Montelionechemical shift assignment
PdbStat5(PDBStat) R. Tejero, G.T. Montelionedata analysis
CNS1.2Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: xplor with hydrogen bond potential refinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 30 / Conformers submitted total number: 20

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