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- PDB-7ae7: Structure of Sedimentibacter hydroxybenzoicus vanillic acid decar... -

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Basic information

Entry
Database: PDB / ID: 7ae7
TitleStructure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in open form, with truncated ShVdcD (V59X)
Components
  • Phenolic acid decarboxylase
  • Protein ShdD
KeywordsLYASE / Decarboxylase / Hetero-complex / UbiD
Function / homology
Function and homology information


protocatechuate decarboxylase / 4-hydroxybenzoate decarboxylase activity / protocatechuate decarboxylase activity / 4-hydroxybenzoate decarboxylase / 4-hydroxy-3-polyprenylbenzoate decarboxylase activity / ubiquinone biosynthetic process / catabolic process / response to toxic substance / metal ion binding / cytosol
Similarity search - Function
Phenolic acid decarboxylase subunit C / : / : / : / : / : / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase N-terminal domain / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase C-terminal domain / UbiD decarboxylyase family / 3-octaprenyl-4-hydroxybenzoate carboxy-lyase Rift-related domain
Similarity search - Domain/homology
Protein ShdD / Phenolic acid decarboxylase
Similarity search - Component
Biological speciesSedimentibacter hydroxybenzoicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsMarshall, S.A. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: To Be Published
Title: Domain mobility and allosteric activation of UbiD decarboxylases
Authors: Marshall, S.A. / Payne, K.A.P. / Leys, D.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phenolic acid decarboxylase
B: Phenolic acid decarboxylase
C: Phenolic acid decarboxylase
D: Phenolic acid decarboxylase
E: Phenolic acid decarboxylase
F: Phenolic acid decarboxylase
a: Protein ShdD
b: Protein ShdD
c: Protein ShdD
d: Protein ShdD
e: Protein ShdD
f: Protein ShdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)364,91923
Polymers364,41112
Non-polymers50711
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area43650 Å2
ΔGint-424 kcal/mol
Surface area103110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.553, 200.945, 201.991
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
Phenolic acid decarboxylase / PAD / 3 / 4-dihydroxybenzoate decarboxylase / 4-dihydroxybenzoate DC / 4-hydroxybenzoate ...PAD / 3 / 4-dihydroxybenzoate decarboxylase / 4-dihydroxybenzoate DC / 4-hydroxybenzoate decarboxylase / 4-hydroxybenzoate DC / Phenolic acid decarboxylase subunit C


Mass: 54020.457 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sedimentibacter hydroxybenzoicus (bacteria)
Gene: shdC, ohb1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9S4M7, protocatechuate decarboxylase, 4-hydroxybenzoate decarboxylase
#2: Protein
Protein ShdD / Phenolic acid decarboxylase subunit D / PAD


Mass: 6714.751 Da / Num. of mol.: 6 / Mutation: V59X
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sedimentibacter hydroxybenzoicus (bacteria)
Gene: shdD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4R102
#3: Chemical
ChemComp-NA / SODIUM ION / Phenolic acid decarboxylase subunit D / PAD


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.87 Å3/Da / Density % sol: 57.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: JCSG-Plus B8 (0.2 M Magnesium chloride hexahydrate, 0.1 M Tris, pH7, 10% PEG 8000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.66→71.43 Å / Num. obs: 119314 / % possible obs: 99.85 % / Redundancy: 21.5 % / Biso Wilson estimate: 37.28 Å2 / CC1/2: 0.988 / Net I/σ(I): 8.25
Reflection shellResolution: 2.66→2.755 Å / Mean I/σ(I) obs: 2.79 / Num. unique obs: 11673 / CC1/2: 0.618

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M1C

5m1c


Resolution: 2.66→71.42 Å / SU ML: 0.3163 / Cross valid method: FREE R-VALUE / σ(F): 1.44 / Phase error: 21.6923
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2268 5824 4.89 %
Rwork0.1799 113353 -
obs0.1822 119177 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.55 Å2
Refinement stepCycle: LAST / Resolution: 2.66→71.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23802 0 11 536 24349
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00324386
X-RAY DIFFRACTIONf_angle_d0.662233350
X-RAY DIFFRACTIONf_chiral_restr0.053807
X-RAY DIFFRACTIONf_plane_restr0.00564365
X-RAY DIFFRACTIONf_dihedral_angle_d5.0143366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.690.38371690.28853199X-RAY DIFFRACTION85.35
2.69-2.720.32561840.26763780X-RAY DIFFRACTION100
2.72-2.750.27741580.24083797X-RAY DIFFRACTION100
2.75-2.780.2931970.22763726X-RAY DIFFRACTION100
2.78-2.820.27831760.22633813X-RAY DIFFRACTION100
2.82-2.860.28462080.22463691X-RAY DIFFRACTION100
2.86-2.90.29541920.22783797X-RAY DIFFRACTION100
2.9-2.940.28371910.22253728X-RAY DIFFRACTION100
2.94-2.990.24971960.21473779X-RAY DIFFRACTION100
2.99-3.040.28992170.21143727X-RAY DIFFRACTION99.97
3.04-3.090.28441970.20723784X-RAY DIFFRACTION100
3.09-3.150.25122230.19073719X-RAY DIFFRACTION100
3.15-3.210.24542100.19363749X-RAY DIFFRACTION100
3.21-3.270.26121690.20063816X-RAY DIFFRACTION100
3.27-3.350.24161630.19753772X-RAY DIFFRACTION100
3.35-3.420.25211920.19313800X-RAY DIFFRACTION100
3.42-3.510.23622140.19083773X-RAY DIFFRACTION100
3.51-3.60.24762000.18483769X-RAY DIFFRACTION100
3.6-3.710.23642010.17693777X-RAY DIFFRACTION100
3.71-3.830.20371770.16243810X-RAY DIFFRACTION100
3.83-3.970.2092170.15123779X-RAY DIFFRACTION100
3.97-4.120.19051720.14393822X-RAY DIFFRACTION100
4.12-4.310.1861730.13853818X-RAY DIFFRACTION100
4.31-4.540.17822140.13663792X-RAY DIFFRACTION100
4.54-4.820.16491960.14243845X-RAY DIFFRACTION100
4.82-5.20.19721850.14923829X-RAY DIFFRACTION100
5.2-5.720.22322230.16813833X-RAY DIFFRACTION100
5.72-6.550.21022020.17863855X-RAY DIFFRACTION100
6.55-8.250.20641960.17053923X-RAY DIFFRACTION100
8.25-71.420.1722120.17464051X-RAY DIFFRACTION98.98
Refinement TLS params.Method: refined / Origin x: -31.0540171644 Å / Origin y: 24.2582848945 Å / Origin z: -43.0570647466 Å
111213212223313233
T0.186477443939 Å20.0337810866907 Å2-0.0172817823457 Å2-0.201123063655 Å2-0.0194749182089 Å2--0.187270162388 Å2
L0.355693165841 °20.0202083998698 °20.0278461156091 °2-0.285728861586 °20.0123204134738 °2--0.355616280718 °2
S0.0332653567817 Å °0.0505335915716 Å °-0.0351183566803 Å °-0.0811406074911 Å °-0.041502907031 Å °-0.0359588190867 Å °0.0638571831181 Å °0.0733863075381 Å °0.00870679340179 Å °
Refinement TLS groupSelection details: all

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