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- PDB-8qoc: Crystal structure of Staphylococcus aureus PLP Synthase (Pdx1) -

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Basic information

Entry
Database: PDB / ID: 8qoc
TitleCrystal structure of Staphylococcus aureus PLP Synthase (Pdx1)
ComponentsPyridoxal 5'-phosphate synthase subunit PdxS
KeywordsTRANSFERASE / Staphylococcus aureus / vitamin B6 / PLP synthase / oligomeric state
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxS/SNZ / PdxS/SNZ N-terminal domain / SOR/SNZ family / PdxS/SNZ family signature. / PdxS/SNZ family profile. / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
PHOSPHATE ION / Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.83 Å
AuthorsUllah, N. / Wrenger, C. / Betzel, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)390715994 Germany
CitationJournal: J.Biol.Chem. / Year: 2024
Title: Structure and dynamics of the staphylococcal pyridoxal 5-phosphate synthase complex reveal transient interactions at the enzyme interface.
Authors: Barra, A.L.C. / Ullah, N. / Brognaro, H. / Gutierrez, R.F. / Wrenger, C. / Betzel, C. / Nascimento, A.S.
History
DepositionSep 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal 5'-phosphate synthase subunit PdxS
B: Pyridoxal 5'-phosphate synthase subunit PdxS
C: Pyridoxal 5'-phosphate synthase subunit PdxS
D: Pyridoxal 5'-phosphate synthase subunit PdxS
E: Pyridoxal 5'-phosphate synthase subunit PdxS
F: Pyridoxal 5'-phosphate synthase subunit PdxS
G: Pyridoxal 5'-phosphate synthase subunit PdxS
H: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,75137
Polymers235,7508
Non-polymers2,00029
Water1,71195
1
A: Pyridoxal 5'-phosphate synthase subunit PdxS
B: Pyridoxal 5'-phosphate synthase subunit PdxS
D: Pyridoxal 5'-phosphate synthase subunit PdxS
E: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules

A: Pyridoxal 5'-phosphate synthase subunit PdxS
B: Pyridoxal 5'-phosphate synthase subunit PdxS
D: Pyridoxal 5'-phosphate synthase subunit PdxS
E: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules

A: Pyridoxal 5'-phosphate synthase subunit PdxS
B: Pyridoxal 5'-phosphate synthase subunit PdxS
D: Pyridoxal 5'-phosphate synthase subunit PdxS
E: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,95563
Polymers353,62512
Non-polymers3,32951
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area50140 Å2
ΔGint-578 kcal/mol
Surface area100860 Å2
2
C: Pyridoxal 5'-phosphate synthase subunit PdxS
F: Pyridoxal 5'-phosphate synthase subunit PdxS
G: Pyridoxal 5'-phosphate synthase subunit PdxS
H: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules

C: Pyridoxal 5'-phosphate synthase subunit PdxS
F: Pyridoxal 5'-phosphate synthase subunit PdxS
G: Pyridoxal 5'-phosphate synthase subunit PdxS
H: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules

C: Pyridoxal 5'-phosphate synthase subunit PdxS
F: Pyridoxal 5'-phosphate synthase subunit PdxS
G: Pyridoxal 5'-phosphate synthase subunit PdxS
H: Pyridoxal 5'-phosphate synthase subunit PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)356,29748
Polymers353,62512
Non-polymers2,67136
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area47410 Å2
ΔGint-473 kcal/mol
Surface area100940 Å2
Unit cell
Length a, b, c (Å)192.419, 192.419, 448.198
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Pyridoxal 5'-phosphate synthase subunit PdxS


Mass: 29468.791 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: pdxS / Production host: Escherichia coli (E. coli) / References: UniProt: P60798

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Non-polymers , 5 types, 124 molecules

#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.4 Å3/Da / Density % sol: 63.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris base (Bicine), NaNO3, NA2HPO4, (NH4)2SO4, P550MME-P20K 30%

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.827→49.8 Å / Num. obs: 76173 / % possible obs: 99.59 % / Redundancy: 10.3 % / Biso Wilson estimate: 56.98 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.1081 / Net I/σ(I): 16.04
Reflection shellResolution: 2.827→2.928 Å / Mean I/σ(I) obs: 3.54 / Num. unique obs: 7248 / CC1/2: 0.954 / % possible all: 98.36

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
XDSdata reduction
SCALAdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.83→49.8 Å / SU ML: 0.3949 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.035
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2602 3810 5 %
Rwork0.2021 72363 -
obs0.205 76173 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.16 Å2
Refinement stepCycle: LAST / Resolution: 2.83→49.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16216 0 99 95 16410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008216497
X-RAY DIFFRACTIONf_angle_d0.989522252
X-RAY DIFFRACTIONf_chiral_restr0.05482519
X-RAY DIFFRACTIONf_plane_restr0.00892966
X-RAY DIFFRACTIONf_dihedral_angle_d6.58142351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.83-2.860.43161340.37412548X-RAY DIFFRACTION96.13
2.86-2.90.41411390.33962634X-RAY DIFFRACTION99.75
2.9-2.940.38481390.31472651X-RAY DIFFRACTION99.5
2.94-2.980.39361400.27652646X-RAY DIFFRACTION99.43
2.98-3.030.33611410.26632681X-RAY DIFFRACTION99.82
3.03-3.070.32011390.25212647X-RAY DIFFRACTION99.79
3.07-3.120.36261410.24262684X-RAY DIFFRACTION99.86
3.12-3.180.35571390.2312638X-RAY DIFFRACTION99.75
3.18-3.240.29551400.21652653X-RAY DIFFRACTION99.47
3.24-3.30.3161420.22652678X-RAY DIFFRACTION99.86
3.3-3.370.31321390.22762673X-RAY DIFFRACTION99.79
3.37-3.440.28391410.24042683X-RAY DIFFRACTION99.89
3.44-3.520.32791410.24732660X-RAY DIFFRACTION99.93
3.52-3.610.28681400.22122662X-RAY DIFFRACTION99.93
3.61-3.70.25171420.2022697X-RAY DIFFRACTION99.89
3.7-3.810.28281410.19712679X-RAY DIFFRACTION99.93
3.81-3.940.25481410.1912686X-RAY DIFFRACTION99.93
3.94-4.080.23981410.18392675X-RAY DIFFRACTION99.96
4.08-4.240.22411420.18292690X-RAY DIFFRACTION99.93
4.24-4.430.22771420.17422699X-RAY DIFFRACTION99.93
4.43-4.670.20931410.16992690X-RAY DIFFRACTION99.96
4.67-4.960.21671420.15852700X-RAY DIFFRACTION100
4.96-5.340.22681430.17612716X-RAY DIFFRACTION99.9
5.34-5.880.28771420.21282701X-RAY DIFFRACTION99.96
5.88-6.730.25611450.20662742X-RAY DIFFRACTION100
6.73-8.470.22081450.16122768X-RAY DIFFRACTION99.97
8.47-49.80.15851480.16062782X-RAY DIFFRACTION97.47

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