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- PDB-6wce: Structure of the periplasmic binding protein P5PA -

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Basic information

Entry
Database: PDB / ID: 6wce
TitleStructure of the periplasmic binding protein P5PA
ComponentsPyridoxal-5-phosphate binding protein A (P5PA)
KeywordsTRANSPORT PROTEIN / type-II periplasmic binding protein / VitaminB6 / nutrition
Function / homologyPYRIDOXAL-5'-PHOSPHATE
Function and homology information
Biological speciesActinobacillus pleuropneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.754 Å
AuthorsPan, C. / Zimmer, A. / Shah, M. / Huynh, M. / Lai, C.C.L. / Sit, B. / Hooda, Y. / Moraes, T.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2018-06546 Canada
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Actinobacillus utilizes a binding protein-dependent ABC transporter to acquire the active form of vitamin B 6 .
Authors: Pan, C. / Zimmer, A. / Shah, M. / Huynh, M.S. / Lai, C.C. / Sit, B. / Hooda, Y. / Curran, D.M. / Moraes, T.F.
History
DepositionMar 30, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxal-5-phosphate binding protein A (P5PA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4062
Polymers39,1591
Non-polymers2471
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, Size-exclusion chromatography with multi-angle light scattering (SEC-MAL) for its homologue AfuA (PDB:4R73)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.468, 42.273, 69.601
Angle α, β, γ (deg.)90.000, 106.818, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb

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Components

#1: Protein Pyridoxal-5-phosphate binding protein A (P5PA)


Mass: 39158.699 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinobacillus pleuropneumoniae (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.85 Å3/Da / Density % sol: 33.54 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.05M potassium thiocyanate, 27.5% PEG MME 2000

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Data collection

DiffractionMean temperature: 105 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.75→66.624 Å / Num. obs: 28927 / % possible obs: 92.82 % / Redundancy: 5.1 % / Biso Wilson estimate: 7.94 Å2 / CC1/2: 0.996 / Net I/σ(I): 24.68
Reflection shellResolution: 1.754→1.817 Å / Num. unique obs: 2856 / CC1/2: 0.985

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4R73

4r73


Resolution: 1.754→66.62 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.8515 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1949 1353 5.03 %
Rwork0.1606 25553 -
obs0.1623 26906 92.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.54 Å2
Refinement stepCycle: LAST / Resolution: 1.754→66.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2454 0 16 241 2711
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00662519
X-RAY DIFFRACTIONf_angle_d0.78653403
X-RAY DIFFRACTIONf_chiral_restr0.2724372
X-RAY DIFFRACTIONf_plane_restr0.0048438
X-RAY DIFFRACTIONf_dihedral_angle_d15.7322952
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.754-1.820.2817840.21121591X-RAY DIFFRACTION58.96
1.82-1.890.23821360.17362529X-RAY DIFFRACTION91.99
1.89-1.980.19971320.15832633X-RAY DIFFRACTION96.24
1.98-2.080.22251450.15622644X-RAY DIFFRACTION96.71
2.08-2.210.19341280.15032647X-RAY DIFFRACTION96.89
2.21-2.380.19371390.16132696X-RAY DIFFRACTION97.16
2.38-2.620.1981530.16932648X-RAY DIFFRACTION97.7
2.62-30.20141390.17772716X-RAY DIFFRACTION97.67
3-3.780.18561510.16252683X-RAY DIFFRACTION97.59
3.78-66.620.15561460.13732766X-RAY DIFFRACTION96.55

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