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- PDB-5mp4: The structure of Pst2p from Saccharomyces cerevisiae -

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Basic information

Entry
Database: PDB / ID: 5mp4
TitleThe structure of Pst2p from Saccharomyces cerevisiae
ComponentsProtoplast secreted protein 2
KeywordsOXIDOREDUCTASE / FMN binding / flavodoxin-like / quinone reduction
Function / homology
Function and homology information


NAD(P)H dehydrogenase (quinone) activity / FMN binding / mitochondrion / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Flavoprotein WrbA-like / NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavodoxin-like domain profile. / Flavodoxin/nitric oxide synthase / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Protoplast secreted protein 2
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.79 Å
AuthorsHromic, A. / Gruber, K.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundW901 Austria
CitationJournal: Biochim. Biophys. Acta / Year: 2017
Title: Structure, biochemical and kinetic properties of recombinant Pst2p from Saccharomyces cerevisiae, a FMN-dependent NAD(P)H:quinone oxidoreductase.
Authors: Koch, K. / Hromic, A. / Sorokina, M. / Strandback, E. / Reisinger, M. / Gruber, K. / Macheroux, P.
History
DepositionDec 15, 2016Deposition site: PDBE / Processing site: PDBE
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 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protoplast secreted protein 2
B: Protoplast secreted protein 2
C: Protoplast secreted protein 2
D: Protoplast secreted protein 2
E: Protoplast secreted protein 2
F: Protoplast secreted protein 2
G: Protoplast secreted protein 2
H: Protoplast secreted protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)168,64416
Polymers167,8858
Non-polymers7608
Water00
1
A: Protoplast secreted protein 2
B: Protoplast secreted protein 2
C: Protoplast secreted protein 2
D: Protoplast secreted protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3228
Polymers83,9424
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11820 Å2
ΔGint-120 kcal/mol
Surface area25460 Å2
MethodPISA
2
E: Protoplast secreted protein 2
F: Protoplast secreted protein 2
G: Protoplast secreted protein 2
H: Protoplast secreted protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,3228
Polymers83,9424
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-119 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.410, 110.560, 223.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Protoplast secreted protein 2


Mass: 20985.580 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Gene: PST2, YDR032C, D3422, YD9673.02C / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q12335
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.91 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% w/v PEG-3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 9, 2014
RadiationMonochromator: Si(111) and Si (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.79→46.17 Å / Num. obs: 43021 / % possible obs: 98.14 % / Redundancy: 4.8 % / Biso Wilson estimate: 66.87 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1041 / Net I/σ(I): 10.2
Reflection shellResolution: 2.79→2.89 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.8343 / Mean I/σ(I) obs: 1.8 / CC1/2: 0.663 / % possible all: 94.46

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3b6i

3b6i


Resolution: 2.79→46.17 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.07
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 2108 4.91 %Random selection
Rwork0.2533 ---
obs0.2549 42973 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.79→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11800 0 40 0 11840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312152
X-RAY DIFFRACTIONf_angle_d0.56516536
X-RAY DIFFRACTIONf_dihedral_angle_d10.9656904
X-RAY DIFFRACTIONf_chiral_restr0.0411792
X-RAY DIFFRACTIONf_plane_restr0.0042136
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7901-2.8550.43961150.38442548X-RAY DIFFRACTION93
2.855-2.92630.41291300.37892658X-RAY DIFFRACTION97
2.9263-3.00550.41631350.35662706X-RAY DIFFRACTION98
3.0055-3.09390.36181400.3282687X-RAY DIFFRACTION99
3.0939-3.19370.3511430.31812714X-RAY DIFFRACTION99
3.1937-3.30780.32871410.29962733X-RAY DIFFRACTION99
3.3078-3.44020.27411360.29982717X-RAY DIFFRACTION99
3.4402-3.59670.31111290.28372663X-RAY DIFFRACTION97
3.5967-3.78630.34161500.27372727X-RAY DIFFRACTION99
3.7863-4.02340.29041340.25782740X-RAY DIFFRACTION99
4.0234-4.33380.28341390.23882775X-RAY DIFFRACTION99
4.3338-4.76950.26111490.22022704X-RAY DIFFRACTION98
4.7695-5.45880.25261580.21582779X-RAY DIFFRACTION99
5.4588-6.87380.27291530.23572810X-RAY DIFFRACTION99
6.8738-46.17960.21111560.19762904X-RAY DIFFRACTION98

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