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- PDB-7plb: Caulobacter crescentus xylonolactonase with D-xylose -

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Basic information

Entry
Database: PDB / ID: 7plb
TitleCaulobacter crescentus xylonolactonase with D-xylose
ComponentsSmp-30/Cgr1 family protein
KeywordsHYDROLASE / XylC / lactonase / mononuclear iron
Function / homology
Function and homology information


xylono-1,5-lactonase / gluconolactonase activity / L-ascorbic acid biosynthetic process / calcium ion binding
Similarity search - Function
Senescence marker protein-30 (SMP-30) / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / Six-bladed beta-propeller, TolB-like
Similarity search - Domain/homology
: / beta-D-xylopyranose / alpha-D-xylopyranose / D-xylonolactone lactonase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPaakkonen, J. / Hakulinen, N. / Rouvinen, J.
Funding support Finland, 4items
OrganizationGrant numberCountry
Academy of Finland118573 Finland
Academy of Finland287241 Finland
Academy of Finland288677 Finland
Academy of Finland322610 Finland
CitationJournal: Protein Sci. / Year: 2022
Title: Three-dimensional structure of xylonolactonase from Caulobacter crescentus: A mononuclear iron enzyme of the 6-bladed beta-propeller hydrolase family.
Authors: Paakkonen, J. / Hakulinen, N. / Andberg, M. / Koivula, A. / Rouvinen, J.
History
DepositionAug 30, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 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: Smp-30/Cgr1 family protein
B: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,63412
Polymers63,3752
Non-polymers1,25910
Water9,962553
1
A: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2906
Polymers31,6881
Non-polymers6025
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3446
Polymers31,6881
Non-polymers6565
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.840, 170.950, 79.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21B-612-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Smp-30/Cgr1 family protein / Xylonolactonase


Mass: 31687.557 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides (strain ATCC 19089 / CB15) (bacteria)
Strain: ATCC 19089 / CB15 / Gene: CC_0820 / Plasmid: pBAT4-XylC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9A9Z1, EC: 3.1.1.68

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Sugars , 2 types, 7 molecules

#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 556 molecules

#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.22 Å3/Da / Density % sol: 44.7 % / Description: Two-dimensional, rectangular
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, HEPES buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.73→85.58 Å / Num. obs: 61016 / % possible obs: 100 % / Redundancy: 2 % / Biso Wilson estimate: 21.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.049 / Rrim(I) all: 0.069 / Net I/σ(I): 9.2
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 2 % / Rmerge(I) obs: 0.719 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 6025 / CC1/2: 0.564 / Rpim(I) all: 0.719 / Rrim(I) all: 1.017 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
GDAdata collection
xia20.5.655-g749651b0-dials-1.11data reduction
DIALS1.11.4-g9c616a499-releasedata scaling
Coot0.8.9.2model building
MR-Rosettaphasing
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GN7

4gn7


Resolution: 1.73→85.47 Å / SU ML: 0.2463 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.2416
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2178 3032 4.97 %Random selection
Rwork0.1807 57948 --
obs0.1825 60980 99.92 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.34 Å2
Refinement stepCycle: LAST / Resolution: 1.73→85.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4442 0 77 553 5072
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354712
X-RAY DIFFRACTIONf_angle_d0.69216457
X-RAY DIFFRACTIONf_chiral_restr0.0477731
X-RAY DIFFRACTIONf_plane_restr0.0053838
X-RAY DIFFRACTIONf_dihedral_angle_d6.2262650
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.760.44841430.40642581X-RAY DIFFRACTION99.71
1.76-1.790.42091350.36882593X-RAY DIFFRACTION99.89
1.79-1.820.32971330.33452627X-RAY DIFFRACTION99.93
1.82-1.850.35271430.31732602X-RAY DIFFRACTION99.82
1.85-1.890.3281350.29282619X-RAY DIFFRACTION99.89
1.89-1.920.33571250.26272597X-RAY DIFFRACTION99.93
1.92-1.970.25631130.23322624X-RAY DIFFRACTION99.89
1.97-2.010.25571310.21272636X-RAY DIFFRACTION100
2.01-2.060.2811540.1932575X-RAY DIFFRACTION99.96
2.06-2.120.25391410.18092619X-RAY DIFFRACTION99.89
2.12-2.180.20331230.17852638X-RAY DIFFRACTION99.96
2.18-2.250.23491440.17382616X-RAY DIFFRACTION99.93
2.25-2.330.22961550.16882602X-RAY DIFFRACTION99.86
2.33-2.420.22221120.1732635X-RAY DIFFRACTION99.96
2.42-2.530.21061510.17272644X-RAY DIFFRACTION99.96
2.53-2.670.22711330.18092628X-RAY DIFFRACTION99.96
2.67-2.830.20181320.18152636X-RAY DIFFRACTION99.93
2.83-3.050.25261310.17362656X-RAY DIFFRACTION99.96
3.05-3.360.21341490.1592654X-RAY DIFFRACTION100
3.36-3.850.15651370.13712674X-RAY DIFFRACTION100
3.85-4.850.13391620.11952684X-RAY DIFFRACTION100
4.85-85.470.20961500.17432808X-RAY DIFFRACTION99.9

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