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- PDB-7plc: Caulobacter crescentus xylonolactonase with D-xylose, P21 space group -

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Basic information

Entry
Database: PDB / ID: 7plc
TitleCaulobacter crescentus xylonolactonase with D-xylose, P21 space group
ComponentsSmp-30/Cgr1 family protein
KeywordsHYDROLASE / XylC / lactonase / mononuclear iron
Function / homology
Function and homology information


xylono-1,5-lactonase / hydrolase activity / metal 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: 2.15 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
C: Smp-30/Cgr1 family protein
D: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,27117
Polymers126,7504
Non-polymers1,52013
Water11,007611
1
A: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1945
Polymers31,6881
Non-polymers5064
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)31,8943
Polymers31,6881
Non-polymers2062
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1945
Polymers31,6881
Non-polymers5064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9904
Polymers31,6881
Non-polymers3023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.776, 82.207, 159.240
Angle α, β, γ (deg.)90.000, 97.686, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 5 and (name N or name...
d_2ens_1(chain "B" and ((resid 5 and (name N or name...
d_3ens_1(chain "C" and (resid 5 through 62 or resid 64...
d_4ens_1(chain "D" and ((resid 5 and (name N or name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1GLNILEA1 - 58
d_12ens_1GLYGLYA60 - 67
d_13ens_1LYSCYSA69 - 145
d_14ens_1SERASPA147 - 274
d_15ens_1ALAVALA276 - 283
d_16ens_1LEUVALA285 - 286
d_21ens_1GLNILEB1 - 58
d_22ens_1GLYGLYB60 - 67
d_23ens_1LYSCYSB69 - 145
d_24ens_1SERASPB147 - 274
d_25ens_1ALAVALB276 - 283
d_26ens_1LEUVALB285 - 286
d_31ens_1GLNILEC1 - 58
d_32ens_1GLYGLYC60 - 67
d_33ens_1LYSCYSC69 - 145
d_34ens_1SERASPC147 - 274
d_35ens_1ALAVALC276 - 283
d_36ens_1LEUVALC285 - 286
d_41ens_1GLNILED1 - 58
d_42ens_1GLYGLYD60 - 67
d_43ens_1LYSCYSD69 - 145
d_44ens_1SERASPD147 - 274
d_45ens_1ALAVALD276 - 283
d_46ens_1LEUVALD285 - 286

NCS oper:
IDCodeMatrixVector
1given(-0.686213133236, -0.222102097657, -0.692663117244), (0.323662249436, -0.946014342538, -0.0173093039111), (-0.651424810752, -0.2360667743, 0.721053530612)-16.6716629429, 60.7104750745, -48.4495364298
2given(0.661672092553, -0.182611044938, 0.727216094571), (-0.187665300242, -0.979352147446, -0.0751738410414), (0.72592821754, -0.0867327940216, -0.682279741323)-41.2068911184, 1.83871341937, 95.1028105979
3given(-0.983523918475, -0.175765525738, 0.0422750724359), (-0.170763202779, 0.980032611515, 0.10186269653), (-0.0593349000499, 0.0929653716707, -0.993899798423)-95.7642095706, -52.7998946948, 111.670730983

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 31687.557 Da / Num. of mol.: 4
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, 8 molecules

#2: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / 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
#3: Sugar ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE / Xylose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / 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, 616 molecules

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


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.28 Å3/Da / Density % sol: 46 % / Description: Two-dimensional, parallelogram-shaped
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, PEG 400, 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: Feb 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.98→158.31 Å / Num. obs: 74548 / % possible obs: 91.7 % / Redundancy: 1.9 % / Biso Wilson estimate: 25.67 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.124 / Rrim(I) all: 0.175 / Net I/σ(I): 3.2
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 2 % / Rmerge(I) obs: 0.752 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 6523 / CC1/2: 0.457 / Rpim(I) all: 0.752 / Rrim(I) all: 1.064 / % possible all: 80.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
GDAdata collection
autoPROC1.0.5 (20181127)data processing
XDSJan 26, 2018 (BUILT 20180808)data reduction
Aimless0.7.3data scaling
pointless1.11.17data scaling
STARANISO2.2.1 (20181029)data scaling
Coot0.8.9.2model building
MR-Rosettaphasing
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GN7

4gn7


Resolution: 2.15→157.81 Å / SU ML: 0.2977 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.9499
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2502 3025 5.07 %Random selection
Rwork0.1978 56625 --
obs0.2005 59650 93.47 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.58 Å2
Refinement stepCycle: LAST / Resolution: 2.15→157.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8800 0 89 611 9500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00269163
X-RAY DIFFRACTIONf_angle_d0.629812520
X-RAY DIFFRACTIONf_chiral_restr0.04891399
X-RAY DIFFRACTIONf_plane_restr0.0041626
X-RAY DIFFRACTIONf_dihedral_angle_d5.16691246
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.751379071363
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.734851947413
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.800065915447
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.180.3956930.31372677X-RAY DIFFRACTION94.35
2.18-2.220.38891250.30382583X-RAY DIFFRACTION95.66
2.22-2.240.3914710.29491294X-RAY DIFFRACTION78.31
2.26-2.30.3161460.28172230X-RAY DIFFRACTION94.96
2.3-2.340.38871530.27352643X-RAY DIFFRACTION98.07
2.34-2.390.33731510.25522715X-RAY DIFFRACTION98.35
2.39-2.440.28791460.23252681X-RAY DIFFRACTION98.71
2.44-2.50.31141280.24092729X-RAY DIFFRACTION98.48
2.5-2.560.30741600.2472708X-RAY DIFFRACTION98.73
2.56-2.630.33611380.24432705X-RAY DIFFRACTION98.96
2.63-2.710.30441340.2412749X-RAY DIFFRACTION98.7
2.71-2.80.29961480.2292693X-RAY DIFFRACTION98.82
2.8-2.90.341170.222762X-RAY DIFFRACTION99.24
2.9-3.010.26121380.21762718X-RAY DIFFRACTION99.1
3.01-3.150.27141590.20532706X-RAY DIFFRACTION98.9
3.15-3.320.24441400.19442731X-RAY DIFFRACTION98.9
3.32-3.520.25051620.1752713X-RAY DIFFRACTION98.39
3.52-3.80.21581350.15742321X-RAY DIFFRACTION84.66
3.8-4.180.17941060.14672025X-RAY DIFFRACTION73
4.18-4.780.14261680.1182667X-RAY DIFFRACTION98.03
4.78-6.020.17921580.14012739X-RAY DIFFRACTION98.91
6.02-157.810.20591490.18432836X-RAY DIFFRACTION99

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