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- PDB-6g81: Solution structure of the Ni metallochaperone HypA from Helicobac... -

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Basic information

Entry
Database: PDB / ID: 6g81
TitleSolution structure of the Ni metallochaperone HypA from Helicobacter pylori
ComponentsHydrogenase maturation factor HypA
KeywordsMETAL BINDING PROTEIN / metallochaperone metal-binding Nickel hydrogenase
Function / homology
Function and homology information


protein modification process => GO:0036211 / nickel cation binding / protein maturation / zinc ion binding
Similarity search - Function
hypothetical protein PF0899 fold - #80 / Hydrogenase maturation factor HypA/HybF / Hydrogenase nickel incorporation protein HypA/HybF, conserved site / Hydrogenase/urease nickel incorporation, metallochaperone, hypA / Hydrogenases expression/synthesis hypA family signature. / hypothetical protein PF0899 fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrogenase maturation factor HypA
Similarity search - Component
Biological speciesHelicobacter pylori J99 (bacteria)
MethodSOLUTION NMR / molecular dynamics
AuthorsSpronk, C.A.E.M. / Zerko, S. / Gorka, M. / Kozminski, W. / Bardiaux, B. / Zambelli, B. / Musiani, F. / Piccioli, M. / Hu, H. / Maroney, M. / Ciurli, S.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2018
Title: Structure and dynamics of Helicobacter pylori nickel-chaperone HypA: an integrated approach using NMR spectroscopy, functional assays and computational tools.
Authors: Spronk, C.A.E.M. / Zerko, S. / Gorka, M. / Kozminski, W. / Bardiaux, B. / Zambelli, B. / Musiani, F. / Piccioli, M. / Basak, P. / Blum, F.C. / Johnson, R.C. / Hu, H. / Merrell, D.S. / Maroney, M. / Ciurli, S.
History
DepositionApr 7, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 8, 2019Group: Data collection / Category: pdbx_nmr_software / Item: _pdbx_nmr_software.name
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_spectrometer
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_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydrogenase maturation factor HypA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2872
Polymers13,2211
Non-polymers651
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7280 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Hydrogenase maturation factor HypA


Mass: 13221.247 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori J99 (bacteria) / Strain: J99 / ATCC 700824 / Gene: hypA, jhp_0803 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A0U5
#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
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic13D HNCO
161isotropic13D HN(CA)CO
131isotropic13D HN(CA)CB
171isotropic13D CBCA(CO)NH
181isotropic13D HBHANH
141isotropic13D HBHA(CO)NH
151isotropic13D (H)CCH-TOCSY
191isotropic32D 1H-13C HSQC aromatic
1101isotropic32D (HB)CB(CGCD)HD
1111isotropic32D (HB)CB(CGCDCE)HE
1121isotropic33D HBCB(CGCD)HD
1131isotropic33D HBCB(CGCDCE)HE
1141isotropic43D 1H-13C NOESY aromatic
1151isotropic34D 13C(ali)-HMQC-NOESY-13C(aro)-HSQC
1161isotropic33D 1H-15N NOESY
1171isotropic34D 13C(ali)-HMQC-NOESY-13C(ali)-HMQC
1181isotropic34D 13C-HMQC-NOESY-15N-HSQC

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Sample preparation

DetailsType: solution
Contents: 1 mM [U-13C; U-15N] HypA, 20 mM HEPES, 200 mM sodium chloride, 1 mM TCEP, 90% H2O/10% D2O
Label: 13C15N_sample / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMHypA[U-13C; U-15N]1
20 mMHEPESnatural abundance1
200 mMsodium chloridenatural abundance1
1 mMTCEPnatural abundance1
Sample conditionsDetails: Protein samples for NMR spectroscopy were constituted by ca. 1 mM [15N/13C]-labeled apo-HpHypA in 20 mM HEPES at pH 7.2 (or pH 6.3), 200 mM NaCl, 1 mM TCEP
Ionic strength: 0.2 Not defined / Label: condition_1 / pH: 7.2 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE9001
Bruker AVANCEBrukerAVANCE9502
Agilent DDR2AgilentDDR28003
Agilent DDR2AgilentDDR26004

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Signal Separation Algorithm (SSA)Stanek, Kosinski, Kozminskiprocessing
CARAKeller and Wuthrichchemical shift assignment
SparkyGoddardchemical shift assignment
TALOS+Cornilescu, Delaglio and Baxdata analysis
YARIABardiaux, Krieger, Spronkstructure calculation
ARIALinge, O'Donoghue and Nilgesstructure calculation
YASARAYASARA Biosciencesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 7
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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