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- PDB-9iz4: Crystal structure of phosphonopyruvate decarboxylase RhiEF from B... -

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Basic information

Entry
Database: PDB / ID: 9iz4
TitleCrystal structure of phosphonopyruvate decarboxylase RhiEF from Bacillus subtilis ATCC6633 in complex with thiamine pyrophosphate
Components
  • Putative phosphonopyruvate decarboxylase alpha subunit
  • Putative phosphonopyruvate decarboxylase beta subunit
KeywordsLYASE / phosphonopyruvate decarboxylase / RhiEF / rhizocticin biosynthesis / thiamine pyrophosphate
Function / homology
Function and homology information


carboxy-lyase activity / thiamine pyrophosphate binding / magnesium ion binding
Similarity search - Function
: / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
SULFOPYRUVATE / THIAMINE DIPHOSPHATE / Putative phosphonopyruvate decarboxylase alpha subunit / Putative phosphonopyruvate decarboxylase beta subunit
Similarity search - Component
Biological speciesBacillus spizizenii ATCC 6633 = JCM 2499 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsNakamura, A. / Kojima, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2024
Title: Structural Analysis of Phosphonopyruvate Decarboxylase RhiEF: First Insights into an Ancestral Heterooligomeric Thiamine Pyrophosphate-Dependent Decarboxylase.
Authors: Nakamura, A. / Shiina, A. / Fukaya, T. / Seki, Y. / Momiyama, M. / Kojima, S.
History
DepositionJul 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative phosphonopyruvate decarboxylase alpha subunit
B: Putative phosphonopyruvate decarboxylase beta subunit
C: Putative phosphonopyruvate decarboxylase alpha subunit
D: Putative phosphonopyruvate decarboxylase beta subunit
E: Putative phosphonopyruvate decarboxylase alpha subunit
F: Putative phosphonopyruvate decarboxylase beta subunit
G: Putative phosphonopyruvate decarboxylase alpha subunit
H: Putative phosphonopyruvate decarboxylase beta subunit
I: Putative phosphonopyruvate decarboxylase alpha subunit
J: Putative phosphonopyruvate decarboxylase beta subunit
K: Putative phosphonopyruvate decarboxylase alpha subunit
L: Putative phosphonopyruvate decarboxylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,66027
Polymers245,45812
Non-polymers3,20215
Water00
1
A: Putative phosphonopyruvate decarboxylase alpha subunit
B: Putative phosphonopyruvate decarboxylase beta subunit
C: Putative phosphonopyruvate decarboxylase alpha subunit
D: Putative phosphonopyruvate decarboxylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7198
Polymers81,8194
Non-polymers8994
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12030 Å2
ΔGint-118 kcal/mol
Surface area23320 Å2
MethodPISA
2
E: Putative phosphonopyruvate decarboxylase alpha subunit
F: Putative phosphonopyruvate decarboxylase beta subunit
G: Putative phosphonopyruvate decarboxylase alpha subunit
H: Putative phosphonopyruvate decarboxylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,05510
Polymers81,8194
Non-polymers1,2356
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-113 kcal/mol
Surface area23690 Å2
MethodPISA
3
I: Putative phosphonopyruvate decarboxylase alpha subunit
J: Putative phosphonopyruvate decarboxylase beta subunit
K: Putative phosphonopyruvate decarboxylase alpha subunit
L: Putative phosphonopyruvate decarboxylase beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8879
Polymers81,8194
Non-polymers1,0675
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12360 Å2
ΔGint-117 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.115, 156.494, 172.971
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Putative phosphonopyruvate decarboxylase alpha subunit


Mass: 20342.178 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus spizizenii ATCC 6633 = JCM 2499 (bacteria)
Gene: rhiE / Production host: Escherichia coli (E. coli) / References: UniProt: D4HRI2
#2: Protein
Putative phosphonopyruvate decarboxylase beta subunit


Mass: 20567.533 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus spizizenii ATCC 6633 = JCM 2499 (bacteria)
Gene: rhiF / Production host: Escherichia coli (E. coli) / References: UniProt: D4HRI3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-TPP / THIAMINE DIPHOSPHATE


Mass: 425.314 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SPV / SULFOPYRUVATE


Mass: 168.125 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H4O6S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350, 0.2M magnesium acetate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→46.79 Å / Num. obs: 41754 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 75.82 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.058 / Rsym value: 0.14 / Net I/σ(I): 10.7
Reflection shellResolution: 3.05→3.17 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 4645 / CC1/2: 0.691 / Rpim(I) all: 0.444 / Rsym value: 1.086

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→43.55 Å / SU ML: 0.3844 / Cross valid method: FREE R-VALUE / σ(F): 1.1 / Phase error: 30.1969 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2763 2106 5.05 %
Rwork0.2322 39556 -
obs0.2345 41662 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 72.27 Å2
Refinement stepCycle: LAST / Resolution: 3.05→43.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16260 0 192 0 16452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002216761
X-RAY DIFFRACTIONf_angle_d0.551522737
X-RAY DIFFRACTIONf_chiral_restr0.04162574
X-RAY DIFFRACTIONf_plane_restr0.00422916
X-RAY DIFFRACTIONf_dihedral_angle_d9.979310005
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.05-3.120.3561400.32552575X-RAY DIFFRACTION100
3.12-3.20.34081430.32762620X-RAY DIFFRACTION100
3.2-3.290.32221170.30392623X-RAY DIFFRACTION100
3.29-3.380.35141160.30942604X-RAY DIFFRACTION100
3.38-3.490.38421180.29412619X-RAY DIFFRACTION100
3.49-3.620.32951560.27632614X-RAY DIFFRACTION99.96
3.62-3.760.29031310.26152621X-RAY DIFFRACTION99.96
3.76-3.930.29051260.24772620X-RAY DIFFRACTION99.93
3.93-4.140.31031410.23822625X-RAY DIFFRACTION100
4.14-4.40.24091550.2142624X-RAY DIFFRACTION99.96
4.4-4.740.24551420.20472632X-RAY DIFFRACTION99.93
4.74-5.210.25691470.19792638X-RAY DIFFRACTION99.93
5.21-5.970.26551610.21452657X-RAY DIFFRACTION100
5.97-7.510.26731680.21992676X-RAY DIFFRACTION100
7.51-43.550.22871450.18642808X-RAY DIFFRACTION98.99

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