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- PDB-4wy0: PdxS (G. stearothermophilus) co-crystallized with R5P in the pres... -

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Basic information

Entry
Database: PDB / ID: 4wy0
TitlePdxS (G. stearothermophilus) co-crystallized with R5P in the presence of ammonia.
Components(Pyridoxal biosynthesis lyase ...) x 3
KeywordsLYASE / 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
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
CACODYLATE ION / PHOSPHATE ION / RIBOSE-5-PHOSPHATE / Pyridoxal 5'-phosphate synthase subunit PdxS
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 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 1.1Apr 19, 2017Group: Refinement description
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Database references / Category: citation / pdbx_audit_support
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Sep 27, 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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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
G: Pyridoxal biosynthesis lyase PdxS
H: Pyridoxal biosynthesis lyase PdxS
I: Pyridoxal biosynthesis lyase PdxS
J: Pyridoxal biosynthesis lyase PdxS
K: Pyridoxal biosynthesis lyase PdxS
L: Pyridoxal biosynthesis lyase PdxS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)399,43231
Polymers396,57012
Non-polymers2,86219
Water22,2671236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44080 Å2
ΔGint-173 kcal/mol
Surface area99900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.680, 107.198, 178.215
Angle α, β, γ (deg.)90.000, 92.240, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11G
21F
31A
41B
51C
61D
71E
81H
91I
101J
111K
121L
12G
22A
32B
42C
52D
62E
72F
82H
92I
102J
112K
122L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111G6 - 80
2111F6 - 80
3111A6 - 80
4111B6 - 80
5111C6 - 80
6111D6 - 80
7111E6 - 80
8111H6 - 80
9111I6 - 80
10111J6 - 80
11111K6 - 80
12111L6 - 80
1121G82 - 270
2121A82 - 270
3121B82 - 270
4121C82 - 270
5121D82 - 270
6121E82 - 270
7121F82 - 270
8121H82 - 270
9121I82 - 270
10121J82 - 270
11121K82 - 270
12121L82 - 270

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.886425, -0.383195, 0.259638), (-0.408302, -0.383101, 0.828567), (-0.218035, -0.840473, -0.49605)0.14052, -0.6677, -87.701103
3given(-0.999976, -0.00216, 0.006636), (0.003045, -0.990649, 0.136404), (0.006279, 0.136421, 0.990631)-119.71608, -12.9039, 1.47043
4given(0.963982, -0.109676, 0.242301), (-0.146104, 0.542884, 0.827001), (-0.222244, -0.832615, 0.507306)7.6004, 24.102249, -43.489521
5given(-0.856779, 0.511358, -0.06666), (0.515667, 0.8485, -0.118894), (-0.004237, -0.136241, -0.990667)-110.062714, 24.674561, -89.45314
6given(-0.882246, 0.433659, 0.183252), (0.40598, 0.503709, 0.762533), (0.238374, 0.747139, -0.620453)-101.646004, 53.384449, -49.730431
7given(0.969822, -0.122413, -0.210858), (-0.116931, 0.525357, -0.842809), (0.213946, 0.842031, 0.495189)-13.74174, -48.89753, -0.74888
8given(0.857963, -0.513709, 0.00156), (-0.513662, -0.857834, 0.016496), (-0.007136, -0.014954, -0.999863)-15.11554, -47.38306, -88.678772
9given(-0.953882, 0.17807, 0.241663), (0.146605, -0.426158, 0.89269), (0.261948, 0.88695, 0.380398)-105.922493, 35.25914, -2.34556
10given(-0.969041, 0.090842, -0.229581), (0.118246, -0.645524, -0.754531), (-0.216743, -0.758319, 0.614797)-128.340561, -42.502811, -37.15905
11given(-0.897197, 0.331725, -0.29154), (0.388539, 0.279087, -0.87815), (-0.20994, -0.901149, -0.379284)-124.987518, -21.98192, -81.891296
12given(0.898663, -0.374567, -0.228263), (-0.380178, -0.405548, -0.831262), (0.218792, 0.833805, -0.506853)-21.68446, -72.926521, -45.11264
13given(1), (1), (1)
14given(-0.999987, 0.000326, -0.005091), (-0.0011, -0.988257, 0.152797), (-0.004981, 0.152801, 0.988244)-119.813271, -13.17676, 0.5748
15given(0.96774, -0.101494, 0.230605), (-0.142541, 0.534168, 0.833275), (-0.207754, -0.839264, 0.502469)7.94804, 23.96615, -43.26899
16given(-0.858314, 0.512085, -0.032648), (0.511472, 0.848714, -0.134466), (-0.04115, -0.132113, -0.99038)-107.287567, 23.098459, -92.55484
17given(-0.890501, 0.406379, 0.204605), (0.406817, 0.509813, 0.758018), (0.203732, 0.758253, -0.619311)-100.027832, 53.142719, -52.681019
18given(0.964437, -0.143879, -0.22172), (-0.112348, 0.536153, -0.836611), (0.239246, 0.831769, 0.500921)-13.7865, -48.665989, 0.21589
19given(0.894055, -0.359128, 0.267754), (-0.405006, -0.392644, 0.825713), (-0.191404, -0.846675, -0.496494)2.31169, -1.14771, -86.957771
20given(0.85788, -0.512366, 0.039031), (-0.512539, -0.858642, -0.006189), (0.036685, -0.014696, -0.999219)-11.98123, -49.13076, -87.176483
21given(-0.96286, 0.147588, 0.226093), (0.147894, -0.412289, 0.898969), (0.225893, 0.899019, 0.375149)-106.038757, 35.24448, -5.64502
22given(-0.962804, 0.112578, -0.245631), (0.114442, -0.653599, -0.748139), (-0.244768, -0.748422, 0.616404)-127.340271, -42.90976, -39.484249
23given(-0.889337, 0.373924, -0.263173), (0.376647, 0.272728, -0.8853), (-0.25926, -0.886454, -0.383385)-120.876381, -23.670759, -86.318604
24given(0.890909, -0.40274, -0.209957), (-0.375941, -0.394516, -0.838466), (0.254853, 0.825928, -0.502884)-20.23572, -73.325127, -43.833961

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Components

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Pyridoxal biosynthesis lyase ... , 3 types, 12 molecules ACEGIJKLBDHF

#1: Protein
Pyridoxal biosynthesis lyase PdxS


Mass: 33115.984 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: pdxS, GK0011 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5L3Y2, Lyases
#2: Protein Pyridoxal biosynthesis lyase PdxS


Mass: 32904.898 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: pdxS, GK0011 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5L3Y2, Lyases
#3: Protein Pyridoxal biosynthesis lyase PdxS


Mass: 32927.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria)
Strain: HTA426 / Gene: pdxS, GK0011 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5L3Y2, Lyases

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Sugars , 1 types, 7 molecules

#6: Sugar
ChemComp-R5P / RIBOSE-5-PHOSPHATE / Ribose 5-phosphate


Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P

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Non-polymers , 4 types, 1248 molecules

#4: Chemical
ChemComp-CAC / CACODYLATE ION / dimethylarsinate / Cacodylic acid


Mass: 136.989 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6AsO2
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: PO4
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1236 / 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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: PEG 8000, Na cacodylate, ammonium 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: Dec 13, 2012 / Details: K-B pair of biomorph mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 158883 / % possible obs: 100 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.093 / Χ2: 1.278 / Net I/av σ(I): 15.485 / Net I/σ(I): 9.6 / Num. measured all: 608487
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.8 % / Rejects: 0

Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.3-2.380.74158581.185100
2.38-2.480.556158071.195100
2.48-2.590.417157841.217100
2.59-2.730.296158171.246100
2.73-2.90.219158791.317100
2.9-3.120.152158551.317100
3.12-3.440.096158311.263100
3.44-3.930.081159171.518100
3.93-4.950.067159861.464100
4.95-500.053161491.05299.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

1znn


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.226 / WRfactor Rwork: 0.1956 / FOM work R set: 0.8166 / SU B: 7.084 / SU ML: 0.166 / SU R Cruickshank DPI: 0.2955 / SU Rfree: 0.2071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.295 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 7970 5 %RANDOM
Rwork0.1913 150841 --
obs0.1929 158883 99.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.46 Å2 / Biso mean: 49.576 Å2 / Biso min: 27.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å2-0 Å2-1.06 Å2
2--1.14 Å20 Å2
3----1.45 Å2
Refinement stepCycle: final / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22595 0 155 1236 23986
Biso mean--77.76 49.7 -
Num. residues----2988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01923019
X-RAY DIFFRACTIONr_bond_other_d0.0020.0222745
X-RAY DIFFRACTIONr_angle_refined_deg1.0851.98131085
X-RAY DIFFRACTIONr_angle_other_deg0.739352174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33852964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.65624.002977
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.354153966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.78215191
X-RAY DIFFRACTIONr_chiral_restr0.0590.23606
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0225884
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024799
X-RAY DIFFRACTIONr_mcbond_it2.434.70611928
X-RAY DIFFRACTIONr_mcbond_other2.434.70611927
X-RAY DIFFRACTIONr_mcangle_it3.9247.03914868
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11G7518.12
12F7514.35
13A7515.88
14B7516.32
15C7514.75
16D7515.25
17E7514.73
18H7516.58
19I7515.43
1107513.71
111G7513.1
112F7519.56
21G28894.89
22A28894.86
23B28893.71
24C28894.65
25D28893.19
26E28894.12
27F28893.73
28H28894.21
29I28893.76
21028893.56
211G28893.68
212A28895.82
LS refinement shellResolution: 2.292→2.352 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 526 -
Rwork0.28 10407 -
all-10933 -
obs--92.97 %

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