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- PDB-7u9c: Crystal Structure of the wild type Escherichia coli Pyridoxal 5'-... -

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Basic information

Entry
Database: PDB / ID: 7u9c
TitleCrystal Structure of the wild type Escherichia coli Pyridoxal 5'-phosphate homeostasis protein (YGGS)
ComponentsPyridoxal phosphate homeostasis protein
KeywordsPROTEIN TRANSPORT / PLP-binding protein / Vitamin B6 / PLP homeostasis
Function / homologyUncharacterized protein family UPF0001 signature. / Pyridoxal phosphate homeostasis protein / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / PLP-binding barrel / pyridoxal phosphate binding / PYRIDOXAL-5'-PHOSPHATE / PHOSPHATE ION / Pyridoxal phosphate homeostasis protein
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsDonkor, A.K. / Ghatge, M.S. / Safo, M.K. / Musayev, F.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM129793 United States
Other governmentS10OD021756 United States
CitationJournal: Protein Sci. / Year: 2022
Title: Characterization of the Escherichia coli pyridoxal 5'-phosphate homeostasis protein (YggS): Role of lysine residues in PLP binding and protein stability.
Authors: Tramonti, A. / Ghatge, M.S. / Babor, J.T. / Musayev, F.N. / di Salvo, M.L. / Barile, A. / Colotti, G. / Giorgi, A. / Paredes, S.D. / Donkor, A.K. / Al Mughram, M.H. / de Crecy-Lagard, V. / ...Authors: Tramonti, A. / Ghatge, M.S. / Babor, J.T. / Musayev, F.N. / di Salvo, M.L. / Barile, A. / Colotti, G. / Giorgi, A. / Paredes, S.D. / Donkor, A.K. / Al Mughram, M.H. / de Crecy-Lagard, V. / Safo, M.K. / Contestabile, R.
History
DepositionMar 10, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Author supporting evidence / Database references / Structure summary
Category: audit_author / citation_author / pdbx_audit_support
Item: _citation_author.name
Revision 1.2Sep 28, 2022Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Nov 9, 2022Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.5Oct 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 phosphate homeostasis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4104
Polymers25,8201
Non-polymers5893
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.188, 124.188, 83.122
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

21A-562-

HOH

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Components

#1: Protein Pyridoxal phosphate homeostasis protein / PLP homeostasis protein


Mass: 25820.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: yggS, yggS_1 / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 / References: UniProt: C3SV52
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES/NaOH pH 7.5, 0.8 NaH2PO4/0.8M KH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Mar 11, 2021 / Details: VariMax TM-VHF Arc)Sec Confocal Optical System
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.1→29.271 Å / Num. obs: 19252 / % possible obs: 100 % / Redundancy: 13.8 % / Biso Wilson estimate: 31.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.019 / Rrim(I) all: 0.071 / Net I/σ(I): 30.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.16140.68415570.9070.1880.71100
8.91-29.27112.20.01528810.0040.01697.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
CrysalisPro41.64.69adata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w8g

1w8g


Resolution: 2.1→29.271 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2184 1003 5.21 %
Rwork0.1777 18235 -
obs0.1799 19238 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.49 Å2 / Biso mean: 34.9622 Å2 / Biso min: 17.92 Å2
Refinement stepCycle: final / Resolution: 2.1→29.271 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1740 0 36 189 1965
Biso mean--56.36 42.25 -
Num. residues----226
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.1001-2.21080.27091430.22372557
2.2108-2.34920.26771430.22222553
2.3492-2.53050.28891550.21042558
2.5305-2.7850.27651300.20622601
2.785-3.18760.22551250.19362617
3.1876-4.01440.19081570.1562610
4.0144-29.2710.18141500.15152739

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