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- PDB-8djf: Crystal structure of RPA3624, a beta-propeller lactonase from Rho... -

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Basic information

Entry
Database: PDB / ID: 8djf
TitleCrystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound tetrahedral intermediate
ComponentsGluconolactonase
KeywordsHYDROLASE / gamma-valerolactone
Function / homologygluconolactonase / gluconolactonase activity / Senescence marker protein-30 (SMP-30) / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / Six-bladed beta-propeller, TolB-like / metal ion binding / (5S)-5-methyloxolane-2,2-diol / Possible gluconolactonase
Function and homology information
Biological speciesRhodopseudomonas palustris CGA009 (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBingman, C.A. / Hall, B.W. / Smith, R.W. / Fox, B.G. / Donohue, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0018409 United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: A broad specificity beta-propeller enzyme from Rhodopseudomonas palustris that hydrolyzes many lactones including gamma-valerolactone.
Authors: Hall, B.W. / Bingman, C.A. / Fox, B.G. / Noguera, D.R. / Donohue, T.J.
History
DepositionJun 30, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 25, 2023Group: 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

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Assembly

Deposited unit
A: Gluconolactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3084
Polymers33,1271
Non-polymers1813
Water2,162120
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.510, 47.510, 199.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Components on special symmetry positions
IDModelComponents
11A-569-

HOH

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Components

#1: Protein Gluconolactonase


Mass: 33126.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris CGA009 (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA3624 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N3R9, gluconolactonase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SGU / (5S)-5-methyloxolane-2,2-diol


Mass: 118.131 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 1.96 Å3/Da / Density % sol: 37.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350, 0.2 M NaCl, 0.1 M NaAcetate pH 4.5, crystals soaked 300 seconds in reservoir supplemented with 20% S-gamma valerolactone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Nov 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.55→38.03 Å / Num. obs: 38815 / % possible obs: 99.6 % / Redundancy: 10.427 % / Biso Wilson estimate: 33.936 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.084 / Χ2: 0.882 / Net I/σ(I): 13.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.55-1.5910.462.9481.227960.6433.09999.1
1.59-1.6410.8732.3161.6227420.812.42999.2
1.64-1.6810.8721.8252.126440.8961.91599.4
1.68-1.7410.8291.3122.8725670.9281.37799.5
1.74-1.7910.8710.9013.8525380.9610.94599.5
1.79-1.8610.910.6245.1724350.9790.65599.6
1.86-1.9310.8610.4357.0623690.9890.45799.6
1.93-210.8120.2799.3122870.9940.29399.7
2-2.0910.7130.21811.4821850.9960.22999.8
2.09-2.210.690.15914.6520890.9960.16899.7
2.2-2.3110.3660.14216.7720000.9960.1599.7
2.31-2.4610.4590.11619.5319120.9960.122100
2.46-2.6210.2630.09521.818200.9970.1100
2.62-2.8410.0460.07925.5216800.9970.08399.9
2.84-3.119.7660.06629.8615400.9970.0799.6
3.11-3.479.3630.05632.5714300.9970.06100
3.47-4.019.2240.05134.8412790.9980.054100
4.01-4.919.3880.04536.9310900.9990.04799.7
4.91-6.948.9390.04635.378880.9980.04999.8
6.94-38.037.7810.04233.095240.9970.04596.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSVERSION Feb 5, 2021data reduction
XSCALEVERSION Feb 5, 2021data scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7ris

7ris


Resolution: 1.55→38.03 Å / SU ML: 0.1727 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.8056
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2115 2998 7.75 %
Rwork0.1781 35667 -
obs0.1806 38665 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.69 Å2
Refinement stepCycle: LAST / Resolution: 1.55→38.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2178 0 10 120 2308
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00962267
X-RAY DIFFRACTIONf_angle_d1.05833088
X-RAY DIFFRACTIONf_chiral_restr0.0663338
X-RAY DIFFRACTIONf_plane_restr0.0117409
X-RAY DIFFRACTIONf_dihedral_angle_d14.5315834
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.580.36011390.35031643X-RAY DIFFRACTION98.78
1.58-1.610.29621370.31131638X-RAY DIFFRACTION98.83
1.61-1.630.36011420.29381681X-RAY DIFFRACTION98.49
1.63-1.670.29291340.26871627X-RAY DIFFRACTION98.99
1.67-1.70.28271420.26071697X-RAY DIFFRACTION99.24
1.7-1.740.27471330.22051642X-RAY DIFFRACTION99.27
1.74-1.780.29411400.22581674X-RAY DIFFRACTION99.34
1.78-1.820.22411430.19721712X-RAY DIFFRACTION99.46
1.82-1.870.25271380.19951652X-RAY DIFFRACTION99.39
1.87-1.930.29811410.2061676X-RAY DIFFRACTION99.45
1.93-1.990.23011420.17981685X-RAY DIFFRACTION99.29
1.99-2.060.22011440.1771703X-RAY DIFFRACTION99.78
2.06-2.140.20381410.17361664X-RAY DIFFRACTION99.56
2.14-2.240.23521370.17671694X-RAY DIFFRACTION99.51
2.24-2.360.2311430.18131708X-RAY DIFFRACTION100
2.36-2.510.20851470.18321732X-RAY DIFFRACTION100
2.51-2.70.20871440.17261688X-RAY DIFFRACTION99.89
2.7-2.970.23721500.18861754X-RAY DIFFRACTION99.79
2.97-3.40.20151450.1671754X-RAY DIFFRACTION99.84
3.4-4.280.1951530.15621765X-RAY DIFFRACTION99.9
4.29-38.030.16931630.16011878X-RAY DIFFRACTION99.22
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.05849811209-0.605546833664-0.4716224499292.52445564080.2287520318532.545463500650.0572816910722-0.1101206782030.09808868594220.00156498971885-0.000858823379465-0.473661540029-0.01069809755170.629750647436-0.002804316761540.2655901214720.04079776890710.04239198651710.3470192222240.04359026730990.33179319583323.8377058878.98574760407-19.4857354929
21.29704142645-0.0821078571599-1.164866786851.98338672880.4549156980543.57956799671-0.02793602704360.0826543129812-0.0645751992635-0.0335798269876-0.1479525135150.1189130176970.330234032544-0.289543410684-0.001132329854110.2435828423340.01679811025760.03297503975870.231828263352-0.01955648584490.2428396930218.081756134316.14148351522-15.9199628385
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 2 through 124 )2 - 1241 - 116
22chain 'A' and (resid 125 through 309 )125 - 309117 - 293

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