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- PDB-4fiq: Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyroc... -

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Basic information

Entry
Database: PDB / ID: 4fiq
TitleCrystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii
ComponentsPyridoxal biosynthesis lyase pdxS
KeywordsLYASE / Pyrococcus horikoshii / pdxS / pyridoxal biosynthesis lyase / pyridoxal 5 -phosphate (PLP)
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
Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / 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 ...Thiazole synthase ThiG / Thiazole biosynthesis protein ThiG / 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 speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMatsuura, A. / Yoon, J.Y. / Yoon, H.J. / Lee, H.H. / Suh, S.W.
CitationJournal: Mol.Cells / Year: 2012
Title: Crystal structure of pyridoxal biosynthesis lyase PdxS from Pyrococcus horikoshii.
Authors: Matsuura, A. / Yoon, J.Y. / Yoon, H.J. / Lee, H.H. / Suh, S.W.
History
DepositionJun 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.2Sep 13, 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
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)222,3926
Polymers222,3926
Non-polymers00
Water6,197344
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17890 Å2
ΔGint-119 kcal/mol
Surface area71120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.295, 178.558, 109.227
Angle α, β, γ (deg.)90.00, 102.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Pyridoxal biosynthesis lyase pdxS


Mass: 37065.309 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea)
Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3
Gene: pdxS, PH1355 / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: O59080, Lyases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 344 / 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: 2.53 Å3/Da / Density % sol: 51.45 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100mM imidazole, 35% 2-methyl-2,4-pentanediol, 200mM MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.0629 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 6, 2005
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0629 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. all: 420103 / Num. obs: 66140 / % possible obs: 100 % / Rmerge(I) obs: 0.08
Reflection shellResolution: 2.61→2.7 Å / Rmerge(I) obs: 0.373 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZNN

1znn


Resolution: 2.7→19.978 Å / SU ML: 0.38 / σ(F): 0 / Phase error: 26.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 3007 5.1 %
Rwork0.1731 --
obs0.1768 58910 97.43 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.594 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-4.9375 Å20 Å27.4692 Å2
2---9.1603 Å20 Å2
3---4.2228 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14784 0 0 344 15128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00915023
X-RAY DIFFRACTIONf_angle_d1.18520233
X-RAY DIFFRACTIONf_dihedral_angle_d16.4485761
X-RAY DIFFRACTIONf_chiral_restr0.0742281
X-RAY DIFFRACTIONf_plane_restr0.0052630
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74420.32461430.23782473X-RAY DIFFRACTION92
2.7442-2.79140.33071320.2382529X-RAY DIFFRACTION92
2.7914-2.8420.36351490.24492552X-RAY DIFFRACTION94
2.842-2.89650.31331620.21792528X-RAY DIFFRACTION94
2.8965-2.95540.26651320.20082652X-RAY DIFFRACTION96
2.9554-3.01950.3081300.20232598X-RAY DIFFRACTION96
3.0195-3.08950.30761210.20162661X-RAY DIFFRACTION97
3.0895-3.16640.27671530.19722605X-RAY DIFFRACTION97
3.1664-3.25170.27361490.20062649X-RAY DIFFRACTION97
3.2517-3.34690.27391530.18512677X-RAY DIFFRACTION98
3.3469-3.45440.24891420.17692711X-RAY DIFFRACTION98
3.4544-3.57720.24991340.17422686X-RAY DIFFRACTION99
3.5772-3.71960.26341350.18332765X-RAY DIFFRACTION100
3.7196-3.88770.23441500.16682682X-RAY DIFFRACTION99
3.8877-4.0910.22941480.15442694X-RAY DIFFRACTION99
4.091-4.34490.22191410.14472721X-RAY DIFFRACTION99
4.3449-4.67630.18561570.13792722X-RAY DIFFRACTION100
4.6763-5.13970.2231470.15382705X-RAY DIFFRACTION100
5.1397-5.86690.26661450.1932782X-RAY DIFFRACTION100
5.8669-7.33040.26191510.19252722X-RAY DIFFRACTION100
7.3304-19.97820.17681330.13482789X-RAY DIFFRACTION100

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