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- PDB-5sxy: The solution NMR structure for the PqqD truncation of Methylobact... -

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Basic information

Entry
Database: PDB / ID: 5sxy
TitleThe solution NMR structure for the PqqD truncation of Methylobacterium extorquens PqqCD representing a functional and stand-alone ribosomally synthesized and post-translational modified (RiPP) recognition element (RRE)
ComponentsBifunctional coenzyme PQQ synthesis protein C/D
KeywordsCHAPERONE / RiPP RRE peptide scaffolding
Function / homology
Function and homology information


pyrroloquinoline-quinone synthase activity / pyrroloquinoline-quinone synthase / pyrroloquinoline quinone biosynthetic process / sulfur compound metabolic process / quinone binding
Similarity search - Function
Coenzyme PQQ synthesis D, bacteria / Coenzyme PQQ synthesis protein D / Coenzyme PQQ synthesis protein D superfamily / Coenzyme PQQ synthesis protein D (PqqD) / Coenzyme PQQ biosynthesis protein C / Pyrroloquinoline-quinone synthase-like / Thiaminase-2/PQQC / TENA/THI-4/PQQC family / Haem oxygenase-like, multi-helical
Similarity search - Domain/homology
Bifunctional coenzyme PQQ synthesis protein C/D
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodSOLUTION NMR / simulated annealing
AuthorsEvans, R.L. / Xia, Y. / Wilmot, C.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-066569 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-039296 United States
Citation
Journal: Biochemistry / Year: 2017
Title: Nuclear Magnetic Resonance Structure and Binding Studies of PqqD, a Chaperone Required in the Biosynthesis of the Bacterial Dehydrogenase Cofactor Pyrroloquinoline Quinone.
Authors: Evans, R.L. / Latham, J.A. / Xia, Y. / Klinman, J.P. / Wilmot, C.M.
#1: Journal: to be published
Title: 1H, 13C, and 15N resonance assignments and secondary structure information for Methylobacterium extorquens PqqD and the complex of PqqD with PqqA
Authors: Evans, R.L. / Latham, J.A. / Klinman, J.P. / Wilmot, C.M. / Xia, Y.
History
DepositionAug 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_audit_support.funding_organization / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bifunctional coenzyme PQQ synthesis protein C/D


Theoretical massNumber of molelcules
Total (without water)10,4221
Polymers10,4221
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Bifunctional coenzyme PQQ synthesis protein C/D / Pyrroloquinoline quinone biosynthesis protein C/D


Mass: 10421.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / AM1) (bacteria)
Strain: ATCC 14718 / DSM 1338 / AM1 / Gene: pqqCD, MexAM1_META1p1749 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q49150, pyrroloquinoline-quinone synthase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic23D HN(CA)CB
121isotropic22D 1H-15N HSQC
131isotropic23D CBCA(CO)NH
141isotropic13D HNCO
151isotropic12D plane of 3D HCACO
161isotropic13D HNHA
171isotropic13D H(CCO)NH
181isotropic13D C(CO)NH
191isotropic13D (H)CCH-TOCSY
1101isotropic12D (HB)CB(CGCD)HD
1111isotropic12D (HB)CB(CGCDCE)HE
1121isotropic12D 1H-13C HSQC aromatic
1131isotropic12D 1H-13C HSQC aliphatic
1141isotropic12D plane of (H)CCH-TOCSY for aromatic ring
1151isotropic23D 15N-edited NOESY
1161isotropic23D 13C-edited NOESY

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Sample preparation

DetailsType: solution / Contents: 4.6 mg/mL [U-13C; U-15N] PqqD, 95% H2O/5% D2O
Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. ...Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. Final concentrations: 4.6 mg/ml (0.37 mM) MexPqqD, 1.1 mM sodium azide, 4.9% D2O).
Label: PqqD / Solvent system: 95% H2O/5% D2O
SampleConc.: 4.6 mg/mL / Component: PqqD / Isotopic labeling: [U-13C; U-15N]
Sample conditionsDetails: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. ...Details: PqqD sample contained 285 micro-L of 5.0 mg/ml (0.40 mM) 13C-, 15N-labeled M.ex.PqqD in 25 mM potassium phosphate, pH 6.5, 7 micro-L of 50 mM sodium azide, and 15 micro-L HPLC grade D2O. Final concentrations: 4.6 mg/ml (0.37 mM) MexPqqD, 1.1 mM sodium azide, 4.9% D2O).
Ionic strength: 25 mM / Label: PqqD / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE IIIBrukerAVANCE III85015 mm TCI CryoProbes including shielded z-gradient
Bruker AVANCE IIIBrukerAVANCE III90025 mm TCI CryoProbes including shielded z-gradient

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin3.1.6Bruker Biospincollection
NMRPipeyear 2012Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3Goddard and Knellerdata analysis
XPLOR-NIH2.37Schwietersstructure calculation
Protein Structure Validation Suite (PSVS)1.5http://psvs-1_5-dev.nesg.org/refinement
RefinementMethod: simulated annealing / Software ordinal: 6
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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