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- PDB-4rhe: Crystal structure of UbiX, an aromatic acid decarboxylase from th... -

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Basic information

Entry
Database: PDB / ID: 4rhe
TitleCrystal structure of UbiX, an aromatic acid decarboxylase from the Colwellia psychrerythraea 34H
Components3-octaprenyl-4-hydroxybenzoate carboxy-lyase
KeywordsLYASE / Rossmann fold / decarboxylase
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / lyase activity / nucleotide binding
Similarity search - Function
Flavin prenyltransferase UbiX-like / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Flavin prenyltransferase UbiX
Similarity search - Component
Biological speciesColwellia psychrerythraea 34H (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.003 Å
AuthorsDo, H. / Kim, S.J. / Lee, C.W. / Kim, H.-W. / Park, H.H. / Kim, H.M. / Park, H. / Park, H.J. / Lee, J.H.
CitationJournal: Sci Rep / Year: 2015
Title: Crystal structure of UbiX, an aromatic acid decarboxylase from the psychrophilic bacterium Colwellia psychrerythraea that undergoes FMN-induced conformational changes.
Authors: Do, H. / Kim, S.J. / Lee, C.W. / Kim, H.W. / Park, H.H. / Kim, H.M. / Park, H. / Park, H. / Lee, J.H.
History
DepositionOct 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2015Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
B: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
C: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
D: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
E: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
F: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,44018
Polymers137,1266
Non-polymers3,31412
Water3,495194
1
A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
B: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
C: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
D: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
E: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
F: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules

A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
B: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
C: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
D: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
E: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
F: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)280,88136
Polymers274,25212
Non-polymers6,62924
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area58350 Å2
ΔGint-483 kcal/mol
Surface area71990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.204, 141.908, 170.069
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
3-octaprenyl-4-hydroxybenzoate carboxy-lyase


Mass: 22854.330 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea 34H (bacteria)
Gene: ubiX, CPS_0408 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q489U8, Lyases; Carbon-carbon lyases; Carboxy-lyases
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 5.8
Details: 200 mM sodium chloride, 100 mM potassium phosphate monobasic/sodium phosphate dibasic, pH 5.8, 11% w/v PEG8000, EVAPORATION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270r / Detector: CCD / Date: Jun 10, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.003→85.539 Å / Num. all: 87139 / Num. obs: 85707 / % possible obs: 98.35 % / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.12
Reflection shellHighest resolution: 2.003 Å / % possible all: 96.37

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.003→76.42 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 4.416 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25024 4216 5 %RANDOM
Rwork0.20168 ---
obs0.20409 79779 96.37 %-
all-87130 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.003→76.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9258 0 216 194 9668
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0199654
X-RAY DIFFRACTIONr_bond_other_d0.0010.029210
X-RAY DIFFRACTIONr_angle_refined_deg2.011.99213110
X-RAY DIFFRACTIONr_angle_other_deg0.91321240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0751206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75324.677372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.296151650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1611542
X-RAY DIFFRACTIONr_chiral_restr0.1150.21494
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110722
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022052
X-RAY DIFFRACTIONr_mcbond_it2.5532.5884842
X-RAY DIFFRACTIONr_mcbond_other2.5522.5874841
X-RAY DIFFRACTIONr_mcangle_it3.5943.866042
X-RAY DIFFRACTIONr_mcangle_other3.5943.866043
X-RAY DIFFRACTIONr_scbond_it3.1693.0834812
X-RAY DIFFRACTIONr_scbond_other3.1743.0874787
X-RAY DIFFRACTIONr_scangle_other4.8244.487033
X-RAY DIFFRACTIONr_long_range_B_refined7.34423.12511488
X-RAY DIFFRACTIONr_long_range_B_other7.34323.12611489
LS refinement shellResolution: 2.003→2.055 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 317 -
Rwork0.256 5952 -
obs--97.74 %

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