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- PDB-3o07: Crystal structure of yeast pyridoxal 5-phosphate synthase Snz1 co... -

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Basic information

Entry
Database: PDB / ID: 3o07
TitleCrystal structure of yeast pyridoxal 5-phosphate synthase Snz1 complexed with substrate G3P
ComponentsPyridoxine biosynthesis protein SNZ1
KeywordsBIOSYNTHETIC PROTEIN / (beta/alpha)8-barrel / pyridoxal 5-phosphate synthase / PLP G3P R5P Sno1
Function / homology
Function and homology information


amine-lyase activity / glutaminase complex / vitamin B6 biosynthetic process / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / glutamine catabolic process / amino acid metabolic 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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GLYCERALDEHYDE-3-PHOSPHATE / Pyridoxal 5'-phosphate synthase subunit SNZ1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTeng, Y.B. / Zhang, X. / Hu, H.X. / Zhou, C.Z.
CitationJournal: Biochem.J. / Year: 2010
Title: Structural insights into the catalytic mechanism of the yeast pyridoxal 5-phosphate synthase Snz1
Authors: Zhang, X. / Teng, Y.B. / Liu, J.P. / He, Y.X. / Zhou, K. / Chen, Y. / Zhou, C.Z.
History
DepositionJul 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2014Group: Database references
Revision 1.3Oct 22, 2014Group: Non-polymer description
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pyridoxine biosynthesis protein SNZ1
B: Pyridoxine biosynthesis protein SNZ1
C: Pyridoxine biosynthesis protein SNZ1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6096
Polymers94,0993
Non-polymers5103
Water13,565753
1
A: Pyridoxine biosynthesis protein SNZ1
B: Pyridoxine biosynthesis protein SNZ1
C: Pyridoxine biosynthesis protein SNZ1
hetero molecules

A: Pyridoxine biosynthesis protein SNZ1
B: Pyridoxine biosynthesis protein SNZ1
C: Pyridoxine biosynthesis protein SNZ1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,21812
Polymers188,1986
Non-polymers1,0206
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area10550 Å2
ΔGint-77 kcal/mol
Surface area65910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.474, 111.972, 158.744
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Pyridoxine biosynthesis protein SNZ1 / PDX1 homolog 1 / p35


Mass: 31366.279 Da / Num. of mol.: 3 / Fragment: residues 15-297
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SNZ1 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: Q03148
#2: Chemical ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE / Glyceraldehyde 3-phosphate


Mass: 170.058 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H2O

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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: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 400, 0.1M Megnesium Chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 95196 / Num. obs: 95196 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 1.8→1.83 Å / % possible all: 99.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3o05

3o05


Resolution: 1.8→44.2 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23583 5006 5 %RANDOM
Rwork0.20342 ---
obs0.20505 95196 99.52 %-
all-95196 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.525 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---0.31 Å20 Å2
3----0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5806 0 30 753 6589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226123
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9878301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0565833
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57125.238210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.985151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0481530
X-RAY DIFFRACTIONr_chiral_restr0.0830.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214464
X-RAY DIFFRACTIONr_mcbond_it0.6491.54037
X-RAY DIFFRACTIONr_mcangle_it1.20826544
X-RAY DIFFRACTIONr_scbond_it1.69832086
X-RAY DIFFRACTIONr_scangle_it3.0484.51757
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 359 -
Rwork0.244 6975 -
obs--99.47 %

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