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- PDB-7ae4: Structure of Sedimentibacter hydroxybenzoicus vanillic acid decar... -

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Basic information

Entry
Database: PDB / ID: 7ae4
TitleStructure of Sedimentibacter hydroxybenzoicus vanillic acid decarboxylase (ShVdcCD) in closed form
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
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Protein ShdD / Phenolic acid decarboxylase
Similarity search - Component
Biological speciesSedimentibacter hydroxybenzoicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.31 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)373,28858
Polymers370,92412
Non-polymers2,36446
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area58930 Å2
ΔGint-635 kcal/mol
Surface area103320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)270.920, 320.550, 326.230
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Space group name HallF22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x,y+1/2,z+1/2
#6: x,-y+1/2,-z+1/2
#7: -x,y+1/2,-z+1/2
#8: -x,-y+1/2,z+1/2
#9: x+1/2,y,z+1/2
#10: x+1/2,-y,-z+1/2
#11: -x+1/2,y,-z+1/2
#12: -x+1/2,-y,z+1/2
#13: x+1/2,y+1/2,z
#14: x+1/2,-y+1/2,-z
#15: -x+1/2,y+1/2,-z
#16: -x+1/2,-y+1/2,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 3 through 6 or (resid 7...
d_2ens_1(chain "B" and (resid 3 through 22 or (resid 23...
d_3ens_1(chain "C" and (resid 3 through 24 or (resid 25...
d_4ens_1(chain "D" and ((resid 3 and (name N or name...
d_5ens_1(chain "E" and ((resid 3 and (name N or name...
d_6ens_1(chain "F" and ((resid 3 and (name N or name...
d_1ens_2chain "a"
d_2ens_2chain "b"
d_3ens_2chain "c"
d_4ens_2chain "d"
d_5ens_2chain "e"
d_6ens_2chain "f"

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1LYSASNA2 - 476
d_21ens_1LYSASNC2 - 476
d_31ens_1LYSASND2 - 476
d_41ens_1LYSASNF2 - 476
d_51ens_1LYSASNH1 - 475
d_61ens_1LYSASNL2 - 476
d_11ens_2METLYSN1 - 67
d_21ens_2METLYSO1 - 67
d_31ens_2METLYSP1 - 67
d_41ens_2METLYSQ1 - 67
d_51ens_2METLYSR1 - 67
d_61ens_2METLYSS1 - 67

NCS ensembles :
ID
ens_1
ens_2

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Components

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Protein , 2 types, 12 molecules ABCDEFabcdef

#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: 7800.174 Da / Num. of mol.: 6
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

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Non-polymers , 7 types, 46 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn

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Details

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: 4.77 Å3/Da / Density % sol: 74.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2M Sodium chloride 0.1M Sodium/potassium phosphate (pH6.2) 50% (v/v) PEG 200

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 1.284 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.284 Å / Relative weight: 1
ReflectionResolution: 3.31→64.05 Å / Num. obs: 104765 / % possible obs: 99.94 % / Redundancy: 7.5 % / Biso Wilson estimate: 126.16 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1062 / Rpim(I) all: 0.04155 / Rrim(I) all: 0.1141 / Net I/σ(I): 13.95
Reflection shellResolution: 3.31→3.428 Å / Rmerge(I) obs: 1.554 / Num. unique obs: 10415 / CC1/2: 0.511 / Rpim(I) all: 0.5936 / Rrim(I) all: 1.665

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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: 3.31→64.05 Å / SU ML: 0.3684 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.4013
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1977 5121 4.89 %
Rwork0.1628 99626 -
obs0.1645 104747 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 130.56 Å2
Refinement stepCycle: LAST / Resolution: 3.31→64.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25588 0 109 0 25697
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003726292
X-RAY DIFFRACTIONf_angle_d0.638935806
X-RAY DIFFRACTIONf_chiral_restr0.04993961
X-RAY DIFFRACTIONf_plane_restr0.0054692
X-RAY DIFFRACTIONf_dihedral_angle_d5.52633526
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.548485430806
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.540530102697
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.400147493268
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.413610087983
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.456949887134
ens_2d_2aX-RAY DIFFRACTIONTorsion NCS0.309074123149
ens_2d_3aX-RAY DIFFRACTIONTorsion NCS0.271765656856
ens_2d_4aX-RAY DIFFRACTIONTorsion NCS0.290954423887
ens_2d_5aX-RAY DIFFRACTIONTorsion NCS0.292638677802
ens_2d_6aX-RAY DIFFRACTIONTorsion NCS0.243020599131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.31-3.350.35391520.31633317X-RAY DIFFRACTION99.94
3.35-3.390.33381490.29773304X-RAY DIFFRACTION100
3.39-3.430.30851780.28573313X-RAY DIFFRACTION100
3.43-3.470.27871680.2593290X-RAY DIFFRACTION99.94
3.47-3.520.30641690.25233285X-RAY DIFFRACTION99.97
3.52-3.570.29421810.2523275X-RAY DIFFRACTION100
3.57-3.620.28051890.24133312X-RAY DIFFRACTION99.97
3.62-3.670.29811800.23793270X-RAY DIFFRACTION100
3.67-3.730.22771670.21183331X-RAY DIFFRACTION100
3.73-3.790.26681840.20263265X-RAY DIFFRACTION100
3.79-3.850.22341800.19383286X-RAY DIFFRACTION100
3.85-3.920.21361850.17073303X-RAY DIFFRACTION99.97
3.92-40.20991790.15593295X-RAY DIFFRACTION99.94
4-4.080.20161660.15463320X-RAY DIFFRACTION100
4.08-4.170.19521740.15433321X-RAY DIFFRACTION100
4.17-4.270.17971810.14583257X-RAY DIFFRACTION100
4.27-4.370.18951770.13043312X-RAY DIFFRACTION100
4.37-4.490.15451520.12873326X-RAY DIFFRACTION100
4.49-4.620.15221680.12193317X-RAY DIFFRACTION99.97
4.62-4.770.16151640.12563314X-RAY DIFFRACTION100
4.77-4.940.15871520.12593333X-RAY DIFFRACTION100
4.94-5.140.16241550.12643346X-RAY DIFFRACTION100
5.14-5.380.16131620.1393349X-RAY DIFFRACTION100
5.38-5.660.18171980.15193304X-RAY DIFFRACTION100
5.66-6.010.20441610.15493355X-RAY DIFFRACTION99.97
6.01-6.480.21491590.15763343X-RAY DIFFRACTION99.97
6.48-7.130.19761590.16463365X-RAY DIFFRACTION100
7.13-8.160.18251900.15433355X-RAY DIFFRACTION100
8.16-10.270.1591810.1333363X-RAY DIFFRACTION99.75
10.27-64.050.20721610.18733500X-RAY DIFFRACTION99.56
Refinement TLS params.Method: refined / Origin x: 29.9533358682 Å / Origin y: 117.460288889 Å / Origin z: 117.970586345 Å
111213212223313233
T0.893394034741 Å2-0.122409555826 Å20.298939035776 Å2-0.873978103045 Å2-0.0775501965232 Å2--0.858421505637 Å2
L0.460759000894 °2-0.0477831726213 °20.0635633902629 °2-0.818129031451 °2-0.16413659621 °2--0.581806506986 °2
S0.0692736390568 Å °-0.126422323337 Å °0.159631650939 Å °-0.277234639091 Å °0.0406825792122 Å °-0.131661108268 Å °-0.071018646262 Å °0.2116739316 Å °-0.107295043465 Å °
Refinement TLS groupSelection details: all

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