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- PDB-2mry: NMR solution structure of copper binding protein in the apo form -

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Basic information

Entry
Database: PDB / ID: 2mry
TitleNMR solution structure of copper binding protein in the apo form
ComponentsUncharacterized protein
Keywordscopper binding protein
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
EfeO-type cupredoxin-like domain / Cupredoxin-like domain / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cupredoxin_1 domain-containing protein / Cupredoxin_1 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailsfewest violations, model 1
AuthorsFu, Y. / Wu, H. / Bruce, K. / Giedroc, D.
CitationJournal: Metallomics / Year: 2016
Title: The S2 Cu(i) site in CupA from Streptococcus pneumoniae is required for cellular copper resistance.
Authors: Fu, Y. / Bruce, K.E. / Wu, H. / Giedroc, D.P.
History
DepositionJul 17, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 12, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
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_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.3May 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)10,8881
Polymers10,8881
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)18 / 100structures with the least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein Uncharacterized protein


Mass: 10887.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: D39 / Gene: spd0634, SPD_0634 / Production host: Escherichia coli (E. coli) / References: UniProt: Q04LG8, UniProt: A0A0M3KKS5*PLUS

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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-15N HSQC
1313D CBCA(CO)NH
1413D CBCANH
1513D HNCO
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D (H)CCH-COSY
11013D HNHA
11113D 1H-15N NOESY
11213D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.4-0.6 mM [U-98% 13C; U-98% 15N] copper binding protein, 10 % [U-99% 2H] D2O, 50 mM sodium phosphate, 50 mM sodium chloride, 5 mM EDTA, 5 mM TCEP, 10 uM DSS, 0.02 % sodium azide, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMentity-1[U-98% 13C; U-98% 15N]0.4-0.61
10 %D2O-2[U-99% 2H]1
50 mMsodium phosphate-31
50 mMsodium chloride-41
5 mMEDTA-51
5 mMTCEP-61
10 uMDSS-71
0.02 %sodium azide-81
Sample conditionsIonic strength: 300 / pH: 6 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent VNMRSAgilentVNMRS8001
Agilent VNMRSAgilentVNMRS6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CcpNmr Analysis2.3.0CCPNpeak picking
CcpNmr Analysis2.3.0CCPNdata analysis
Sparky2.6Goddardchemical shift assignment
Sparky2.6Goddardpeak picking
NMRPipe8.1Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PSVS1.5Bhattacharya and Montelionestructure validation
PINE2Bahrami, Markley, Assadi, and Eghbalniachemical shift assignment
X-PLOR NIH2.36Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 2201 / NOE intraresidue total count: 347 / NOE long range total count: 1067 / NOE medium range total count: 248 / NOE sequential total count: 539 / Protein phi angle constraints total count: 65 / Protein psi angle constraints total count: 65
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 18

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