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- PDB-6bqs: HusA haemophore from Porphyromonas gingivalis -

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Basic information

Entry
Database: PDB / ID: 6bqs
TitleHusA haemophore from Porphyromonas gingivalis
Componentshypothetical protein PG_2227
KeywordsHEME BINDING PROTEIN / haem binding protein
Function / homologyTPR domain protein
Function and homology information
Biological speciesPorphyromonas gingivalis W83 (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsGell, D.A. / Kwan, A.H. / Horne, J. / Hugrass, B.M. / Collins, D.A.T.
CitationJournal: Nat Commun / Year: 2018
Title: Structural properties of a haemophore facilitate targeted elimination of the pathogen Porphyromonas gingivalis.
Authors: Gao, J.L. / Kwan, A.H. / Yammine, A. / Zhou, X. / Trewhella, J. / Hugrass, B.M. / Collins, D.A.T. / Horne, J. / Ye, P. / Harty, D. / Nguyen, K.A. / Gell, D.A. / Hunter, N.
History
DepositionNov 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity.formula_weight
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein PG_2227


Theoretical massNumber of molelcules
Total (without water)21,7461
Polymers21,7461
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11360 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)21 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein hypothetical protein PG_2227


Mass: 21745.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis W83 (bacteria)
Strain: ATCC BAA-308 / W83 / Gene: PG_2227 / Plasmid: pET24d / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Strain B / References: UniProt: Q7MSY3

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic32D NOESY
131isotropic23D 1H-13C NOESY aliphatic
143isotropic23D 1H-13C NOESY aliphatic
151isotropic23D 1H-15N NOESY
161isotropic23D 1H-13C NOESY aromatic
173isotropic23D 1H-13C NOESY aromatic
184isotropic22D NOESY
291isotropic23D HNCA
2101isotropic33D HN(CA)CB
2111isotropic33D CBCA(CO)NH
2121isotropic33D HNCO
2131isotropic33D HBHA(CO)NH
2141isotropic33D H(CCO)NH
2151isotropic33D C(CO)NH
2161isotropic33D (HB)CB(CGCD)HD
2171isotropic33D HBCBCGCDHDCEHE
1182isotropic32D 1H-1H TOCSY
1192isotropic32D 1H-1H COSY
2201isotropic33D 1H-15N NOESY
1213isotropic23D (H)CCH-TOCSY
1223isotropic23D CCH-TOCSY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11.5 mM [U-13C; U-15N] HusA, hypothetical protein PG_2227, 10 mM sodium phosphate, 95% H2O/5% D2O15N_13C_sample95% H2O/5% D2O
solid21 mM HusA, hypothetical protein PG_2227, 10 mM sodium phosphate, 100% D2Onatural_abundance1100% D2O
solution31.5 mM [U-13C; U-15N] HusA, hypothetical protein PG_2227, 10 mM sodium phosphate, 100% D2O15N_13C_sample2100% D2O
solution41 mM HusA, hypothetical protein PG_2227, 10 mM sodium phosphate, 95% H2O/5% D2Onatural_abundance295% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.5 mMHusA, hypothetical protein PG_2227[U-13C; U-15N]1
10 mMsodium phosphatenatural abundance1
1 mMHusA, hypothetical protein PG_2227natural abundance2
10 mMsodium phosphatenatural abundance2
1.5 mMHusA, hypothetical protein PG_2227[U-13C; U-15N]3
10 mMsodium phosphatenatural abundance3
1 mMHusA, hypothetical protein PG_2227natural abundance4
10 mMsodium phosphatenatural abundance4
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
10.01 Mconditions_16.91 atm308 K
20.01 Mconditions_26.91 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II8002
Bruker AVANCE IIBrukerAVANCE II6003

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Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
TopSpinBruker Biospinprocessing
SparkyGoddardchemical shift assignment
CYANAGuntert, Mumenthaler, and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra, and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 21

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