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- PDB-4rhf: Crystal structure of UbiX mutant V47S from Colwellia psychrerythr... -

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Basic information

Entry
Database: PDB / ID: 4rhf
TitleCrystal structure of UbiX mutant V47S from Colwellia psychrerythraea 34H
Components3-octaprenyl-4-hydroxybenzoate carboxy-lyase
KeywordsLYASE / Rossmann fold / decarboxylation
Function / homology
Function and homology information


flavin prenyltransferase / flavin prenyltransferase activity / carboxy-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 prenyltransferase UbiX
Similarity search - Component
Biological speciesColwellia psychrerythraea 34H (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.764 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

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Assembly

Deposited unit
A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0343
Polymers22,8421
Non-polymers1922
Water97354
1
A: 3-octaprenyl-4-hydroxybenzoate carboxy-lyase
hetero molecules
x 12


Theoretical massNumber of molelcules
Total (without water)276,41336
Polymers274,10712
Non-polymers2,30624
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,-y-1,z1
crystal symmetry operation3_454-x-1,y,-z-11
crystal symmetry operation4_544x,-y-1,-z-11
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_544z,-x-1,-y-11
crystal symmetry operation7_445-z-1,-x-1,y1
crystal symmetry operation8_454-z-1,x,-y-11
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_454-y-1,z,-x-11
crystal symmetry operation11_544y,-z-1,-x-11
crystal symmetry operation12_445-y-1,-z-1,x1
Buried area42190 Å2
ΔGint-522 kcal/mol
Surface area78080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.600, 97.600, 97.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number195
Space group name H-MP23

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Components

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


Mass: 22842.277 Da / Num. of mol.: 1 / Mutation: V47S
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.39 Å3/Da / Density % sol: 63.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1 M tri-sodium citrate, pH 5.4, 0.5 M ammonium sulfate, 1.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97952 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 7, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97952 Å / Relative weight: 1
ReflectionResolution: 1.764→97.6 Å / Num. all: 30802 / Num. obs: 30737 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 40.5 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 26.8
Reflection shellResolution: 1.764→1.86 Å / Redundancy: 39.9 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 13.7 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MERLOTphasing
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.764→97.6 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.892 / SU B: 2.216 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25669 1549 5 %RANDOM
Rwork0.23658 ---
obs0.23759 29186 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.39 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.764→97.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1522 0 10 54 1586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0191558
X-RAY DIFFRACTIONr_bond_other_d0.0010.021500
X-RAY DIFFRACTIONr_angle_refined_deg2.2291.9732110
X-RAY DIFFRACTIONr_angle_other_deg0.9833462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0895199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.0524.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.87915273
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.725157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2245
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211740
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2762.249799
X-RAY DIFFRACTIONr_mcbond_other2.2662.247798
X-RAY DIFFRACTIONr_mcangle_it3.1763.364997
X-RAY DIFFRACTIONr_mcangle_other3.2533.403998
X-RAY DIFFRACTIONr_scbond_it2.972.648759
X-RAY DIFFRACTIONr_scbond_other3.0312.706752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2983.9151102
X-RAY DIFFRACTIONr_long_range_B_refined5.54319.1151735
X-RAY DIFFRACTIONr_long_range_B_other5.54519.0471715
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.764→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 112 -
Rwork0.243 2149 -
obs--100 %

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