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- PDB-3o06: Crystal Structure of yeast pyridoxal 5-phosphate synthase Snz1 -

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Basic information

Entry
Database: PDB / ID: 3o06
TitleCrystal Structure of yeast pyridoxal 5-phosphate synthase Snz1
ComponentsPyridoxine biosynthesis protein SNZ1
KeywordsBIOSYNTHETIC PROTEIN / (beta/alpha)8-barrel / pyridoxal 5-phosphate synthase / PLP Sno1 G3P R5P
Function / homology
Function and homology information


vitamin B6 biosynthetic process / amine-lyase activity / glutaminase complex / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic process / L-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
Pyridoxal 5'-phosphate synthase subunit SNZ1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsTeng, Y.B. / Zhang, X. / Zhou, C.Z. / Hu, H.X.
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 1.3Nov 1, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)94,0993
Polymers94,0993
Non-polymers00
Water1,36976
1
A: Pyridoxine biosynthesis protein SNZ1
B: Pyridoxine biosynthesis protein SNZ1
C: Pyridoxine biosynthesis protein SNZ1

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


Theoretical massNumber of molelcules
Total (without water)188,1986
Polymers188,1986
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area10640 Å2
ΔGint-74 kcal/mol
Surface area63850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.313, 110.376, 156.393
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.72 Å3/Da / Density % sol: 54.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 400, 0.1M Megnesium Cloride, 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: Dec 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→110.38 Å / Num. all: 43496 / Num. obs: 43496 / % possible obs: 92.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.35→2.41 Å / % possible all: 91.4

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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: 1znn

1znn


Resolution: 2.35→110.38 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.896 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 9.204 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R: 0.272 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25126 2175 5 %RANDOM
Rwork0.20409 ---
obs0.20646 41124 99.55 %-
all-43299 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 106.72 Å2 / Biso mean: 41.645 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.26 Å2
Refinement stepCycle: LAST / Resolution: 2.35→110.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5799 0 0 76 5875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225670
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.9827640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6895741
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26925.673208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.838151067
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8681527
X-RAY DIFFRACTIONr_chiral_restr0.1320.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214075
X-RAY DIFFRACTIONr_mcbond_it1.2881.53707
X-RAY DIFFRACTIONr_mcangle_it2.31725973
X-RAY DIFFRACTIONr_scbond_it3.46531963
X-RAY DIFFRACTIONr_scangle_it5.84.51667
LS refinement shellResolution: 2.353→2.414 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 137 -
Rwork0.211 2936 -
all-3073 -
obs--97.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0583-0.08160.2330.594-0.00191.189-0.02150.0162-0.01640.05310.03390.0651-0.08130.0576-0.01250.0219-0.02850.01040.0834-0.01790.022720.49733.75318.425
20.28390.0790.04270.73720.77521.7225-0.0389-0.0577-0.0201-0.13550.05740.0263-0.24340.1173-0.01850.052-0.0223-0.00530.03720.01460.013820.49433.041-19.715
30.20120.14520.10832.64920.54390.5805-0.0292-0.02540.0350.21380.03510.17230.0472-0.0424-0.00590.02740.00280.00610.02890.00980.041139.01954.475-40.428
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A17 - 46
2X-RAY DIFFRACTION1A56 - 270
3X-RAY DIFFRACTION2B17 - 46
4X-RAY DIFFRACTION2B56 - 270
5X-RAY DIFFRACTION3C17 - 46
6X-RAY DIFFRACTION3C56 - 270

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