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- PDB-7pld: Caulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrro... -

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Basic information

Entry
Database: PDB / ID: 7pld
TitleCaulobacter crescentus xylonolactonase with (R)-4-hydroxy-2-pyrrolidone
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
(R)-4-hydroxy-2-pyrrolidone / : / D-xylonolactone lactonase
Similarity search - Component
Biological speciesCaulobacter vibrioides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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)63,9929
Polymers63,3752
Non-polymers6177
Water10,431579
1
A: Smp-30/Cgr1 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8453
Polymers31,6881
Non-polymers1572
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)32,1486
Polymers31,6881
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.747, 171.729, 79.254
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 4 through 68 or resid 70...
d_2ens_1(chain "B" and (resid 4 or (resid 5 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1ALAPHEA1 - 65
d_12ens_1VALGLUA67 - 87
d_13ens_1GLUCYSA89 - 146
d_14ens_1SERGLUA148 - 171
d_15ens_1GLYSERA173 - 176
d_16ens_1LYSVALA178 - 223
d_17ens_1ARGVALA225 - 287
d_21ens_1ALAPHEB3 - 67
d_22ens_1VALGLUB69 - 89
d_23ens_1GLUCYSB91 - 148
d_24ens_1SERGLUB150 - 173
d_25ens_1GLYSERB175 - 178
d_26ens_1LYSVALB180 - 225
d_27ens_1ARGVALB227 - 289

NCS oper: (Code: givenMatrix: (0.909397812531, 0.214862790836, 0.356131435959), (-0.152992667138, 0.969007624706, -0.19395222882), (-0.386767194015, 0.121894234385, 0.914085845672)Vector: -14. ...NCS oper: (Code: given
Matrix: (0.909397812531, 0.214862790836, 0.356131435959), (-0.152992667138, 0.969007624706, -0.19395222882), (-0.386767194015, 0.121894234385, 0.914085845672)
Vector: -14.918473698, -34.5847633042, 8.22578638576)

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Components

#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
#2: Chemical
ChemComp-7UK / (R)-4-hydroxy-2-pyrrolidone / (4R)-4-oxidanylpyrrolidin-2-one / (R)-4-hydroxypyrrolidin-2-one


Mass: 101.104 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H7NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.3 % / 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: Feb 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.64→85.98 Å / Num. obs: 73394 / % possible obs: 99.3 % / Redundancy: 2 % / Biso Wilson estimate: 20.43 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.053 / Rrim(I) all: 0.075 / Net I/σ(I): 8.3
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 2 % / Rmerge(I) obs: 0.905 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 6987 / CC1/2: 0.439 / Rpim(I) all: 0.905 / Rrim(I) all: 1.279 / % possible all: 95.5

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Processing

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

4gn7


Resolution: 1.7→78.14 Å / SU ML: 0.2423 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.97
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2343 3292 5 %Random selection
Rwork0.1936 62572 --
obs0.1956 65864 99.65 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→78.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4432 0 37 579 5048
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00564627
X-RAY DIFFRACTIONf_angle_d0.81476326
X-RAY DIFFRACTIONf_chiral_restr0.055700
X-RAY DIFFRACTIONf_plane_restr0.0064831
X-RAY DIFFRACTIONf_dihedral_angle_d6.365640
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.993661628701 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.43621360.38672592X-RAY DIFFRACTION99.13
1.72-1.750.39391410.37252541X-RAY DIFFRACTION98.42
1.75-1.780.37671260.33062565X-RAY DIFFRACTION99.52
1.78-1.810.34861400.30782588X-RAY DIFFRACTION99.67
1.81-1.840.3281230.30482578X-RAY DIFFRACTION99.59
1.84-1.870.31961320.30742599X-RAY DIFFRACTION99.85
1.87-1.910.34061570.30212558X-RAY DIFFRACTION99.49
1.91-1.950.38271410.33992571X-RAY DIFFRACTION99.74
1.95-1.990.28061440.22692584X-RAY DIFFRACTION99.74
1.99-2.030.25991360.19762588X-RAY DIFFRACTION99.82
2.03-2.090.25641310.18632620X-RAY DIFFRACTION99.93
2.09-2.140.2391380.18652588X-RAY DIFFRACTION99.96
2.14-2.20.27891470.1942577X-RAY DIFFRACTION100
2.2-2.280.35231200.29222570X-RAY DIFFRACTION98.39
2.28-2.360.23821410.19542609X-RAY DIFFRACTION99.82
2.36-2.450.26051230.1892627X-RAY DIFFRACTION99.89
2.45-2.560.23771590.18592579X-RAY DIFFRACTION100
2.56-2.70.24211440.192604X-RAY DIFFRACTION99.93
2.7-2.870.22541440.18592617X-RAY DIFFRACTION99.93
2.87-3.090.19911320.18172640X-RAY DIFFRACTION99.96
3.09-3.40.19611330.16192637X-RAY DIFFRACTION99.86
3.4-3.890.19771350.15122657X-RAY DIFFRACTION99.57
3.89-4.90.1451360.1212686X-RAY DIFFRACTION99.89
4.9-78.140.17791330.16172797X-RAY DIFFRACTION99.56

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