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- PDB-4wxz: PdxS (G. stearothermophilus) co-crystallized with R5P -

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Basic information

Entry
Database: PDB / ID: 4wxz
TitlePdxS (G. stearothermophilus) co-crystallized with R5P
ComponentsPyridoxal biosynthesis lyase PdxS
KeywordsTRANSFERASE / beta/alpha barrel / pyridoxal 5-phosphate / glutamine amidotransferase / vitamin b6
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / pyridoxine biosynthetic 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 PdxS
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSmith, J.L. / Smith, A.M.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Crystal structures capture three states in the catalytic cycle of a pyridoxal phosphate (PLP) synthase.
Authors: Smith, A.M. / Brown, W.C. / Harms, E. / Smith, J.L.
History
DepositionNov 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Mar 11, 2015Group: Database references
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _citation.title ..._citation.journal_id_CSD / _citation.title / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
D: Pyridoxal biosynthesis lyase PdxS
E: Pyridoxal biosynthesis lyase PdxS
F: Pyridoxal biosynthesis lyase PdxS


Theoretical massNumber of molelcules
Total (without water)199,5366
Polymers199,5366
Non-polymers00
Water3,423190
1
A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
D: Pyridoxal biosynthesis lyase PdxS
E: Pyridoxal biosynthesis lyase PdxS
F: Pyridoxal biosynthesis lyase PdxS

A: Pyridoxal biosynthesis lyase PdxS
B: Pyridoxal biosynthesis lyase PdxS
C: Pyridoxal biosynthesis lyase PdxS
D: Pyridoxal biosynthesis lyase PdxS
E: Pyridoxal biosynthesis lyase PdxS
F: Pyridoxal biosynthesis lyase PdxS


Theoretical massNumber of molelcules
Total (without water)399,07212
Polymers399,07212
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+2/31
Buried area37650 Å2
ΔGint-147 kcal/mol
Surface area99170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.785, 179.785, 104.568
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

21A-316-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
31C
41D
51E
61F
12B
22A
32C
42D
52E
62F
13B
23A
33C
43D
53E
63F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111B10 - 45
2111A10 - 45
3111C10 - 45
4111D10 - 45
5111E10 - 45
6111F10 - 45
1121B60 - 80
2121A60 - 80
3121C60 - 80
4121D60 - 80
5121E60 - 80
6121F60 - 80
1131B82 - 265
2131A82 - 265
3131C82 - 265
4131D82 - 265
5131E82 - 265
6131F82 - 265

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.535553, -0.843117, -0.048349), (0.840712, 0.537693, -0.063949), (0.079913, -0.0064, 0.996781)117.889503, 98.141243, 1.88124
3given(-0.487302, 0.872858, 0.025611), (0.8688, 0.481668, 0.114814), (0.08788, 0.0782, -0.993057)-179.425919, 100.599403, 58.416611
4given(-0.999751, 0.022126, -0.002929), (0.021592, 0.992056, 0.123928), (0.005648, 0.123834, -0.992287)-61.268009, -2.37425, 49.371361
5given(0.474795, 0.87859, 0.051481), (-0.878179, 0.476808, -0.038157), (-0.058071, -0.027093, 0.997945)-154.621445, 57.751911, 2.35437
6given(-0.523802, -0.849751, -0.059618), (-0.850774, 0.518363, 0.086502), (-0.042602, 0.096032, -0.994466)90.235626, 47.797619, 53.246429
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Pyridoxal biosynthesis lyase PdxS


Mass: 33255.992 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: pdxS, GK0011 / Plasmid: pETTEV281 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5L3Y2, Lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.5 Å3/Da / Density % sol: 50.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, Na cacodylate, lithium citrate / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 6, 2013 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 104026 / % possible obs: 100 % / Redundancy: 5.9 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.123 / Χ2: 1.432 / Net I/av σ(I): 17 / Net I/σ(I): 8.7 / Num. measured all: 611844
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.85.80.8103901.344100
2.8-2.915.90.619104521.314100
2.91-3.045.90.457103761.326100
3.04-3.25.90.32104361.404100
3.2-3.45.90.214103631.431100
3.4-3.665.90.157104251.497100
3.66-4.035.90.117103791.567100
4.03-4.625.90.096103891.791100
4.62-5.815.90.076104221.445100
5.81-505.90.056103941.20299.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
PHASER2.5.2phasing
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNN

1znn


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 13.197 / SU ML: 0.267 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.877 / ESU R Free: 0.337 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2587 2728 5.1 %RANDOM
Rwork0.2163 50930 --
obs0.2185 50930 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 156.56 Å2 / Biso mean: 63.387 Å2 / Biso min: 21.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å2-0.71 Å2-0 Å2
2---1.43 Å20 Å2
3---4.64 Å2
Refinement stepCycle: final / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11232 0 0 190 11422
Biso mean---46.68 -
Num. residues----1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01911376
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211142
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.98715381
X-RAY DIFFRACTIONr_angle_other_deg0.815325558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90851462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89323.971481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.805151906
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7121594
X-RAY DIFFRACTIONr_chiral_restr0.0680.21786
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112788
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022362
X-RAY DIFFRACTIONr_mcbond_it4.2236.1445884
X-RAY DIFFRACTIONr_mcbond_other4.2196.1445883
X-RAY DIFFRACTIONr_mcangle_it6.4499.1987334
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11B36625.55
12A36621.24
13C36611.41
14D3666.82
15E36617.56
16F36636.18
21B31423.92
22A31418.31
23C31412.46
24D31413.89
25E31411.25
26F31433.67
31B282814.98
32A282818.8
33C282813.89
34D28289.79
35E282817.31
36F282828.32
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 205 -
Rwork0.283 3694 -
all-3899 -
obs--99.24 %

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