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- PDB-7ris: Crystal structure of RPA3624, a beta-propeller lactonase from Rho... -

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Basic information

Entry
Database: PDB / ID: 7ris
TitleCrystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound phosphate
ComponentsBeta-propeller lactonase
KeywordsHYDROLASE / gamma-valerolactone
Function / homology
Function and homology information


gluconolactonase / gluconolactonase 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
PHOSPHATE ION / Possible gluconolactonase
Similarity search - Component
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.72 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
DepositionJul 20, 2021Deposition 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 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-propeller lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0744
Polymers32,9161
Non-polymers1583
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.540, 44.540, 189.950
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-554-

HOH

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Components

#1: Protein Beta-propeller lactonase / Possible gluconolactonase


Mass: 32915.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodopseudomonas palustris (strain ATCC BAA-98 / CGA009) (phototrophic)
Strain: ATCC BAA-98 / CGA009 / Gene: RPA3624 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6N3R9, gluconolactonase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals were grown in a MRC SD2 microplate, set with a TTP Labtech Mosquito crystallization robot. In the crystallization experiment leading to the crystal used for data collection, 200 nL ...Details: Crystals were grown in a MRC SD2 microplate, set with a TTP Labtech Mosquito crystallization robot. In the crystallization experiment leading to the crystal used for data collection, 200 nL of protein solution at 10.5 mg/mL was combined with 250 nL reservoir solution, composed of 20% PEG3350, 0.2M CaCl2, 0.1M bistris buffer pH 6.5. Crystals were cryopreserved by soaking in reservoir solution supplemented to 30% PEG3350 and immersion in liquid nitrogen

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.03329 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03329 Å / Relative weight: 1
ReflectionResolution: 1.72→35.74 Å / Num. obs: 24269 / % possible obs: 99.62 % / Redundancy: 19.7 % / Biso Wilson estimate: 28 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08686 / Rpim(I) all: 0.02012 / Rrim(I) all: 0.08923 / Net I/σ(I): 20.07
Reflection shellResolution: 1.72→1.782 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.4783 / Mean I/σ(I) obs: 1.72 / Num. unique obs: 2381 / CC1/2: 0.916 / CC star: 0.978 / Rpim(I) all: 0.3297 / Rrim(I) all: 1.511 / % possible all: 99.29

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.72→35.74 Å / SU ML: 0.1509 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.7016
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2011 1995 8.25 %
Rwork0.1788 22196 -
obs0.1807 24191 99.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.13 Å2
Refinement stepCycle: LAST / Resolution: 1.72→35.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2174 0 7 114 2295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042245
X-RAY DIFFRACTIONf_angle_d0.70473054
X-RAY DIFFRACTIONf_chiral_restr0.0488335
X-RAY DIFFRACTIONf_plane_restr0.0053406
X-RAY DIFFRACTIONf_dihedral_angle_d13.3367824
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.760.33791380.27391542X-RAY DIFFRACTION99
1.76-1.810.29161340.24871516X-RAY DIFFRACTION99.22
1.81-1.860.26351420.2311565X-RAY DIFFRACTION99.59
1.86-1.920.21571400.20911571X-RAY DIFFRACTION99.65
1.92-1.990.22641370.19111528X-RAY DIFFRACTION99.11
1.99-2.070.24431390.18631551X-RAY DIFFRACTION99.47
2.07-2.170.2061430.18341559X-RAY DIFFRACTION99.59
2.17-2.280.24481400.181597X-RAY DIFFRACTION99.83
2.28-2.420.24541390.18491577X-RAY DIFFRACTION99.94
2.42-2.610.2341460.1921591X-RAY DIFFRACTION99.88
2.61-2.870.21371450.18611594X-RAY DIFFRACTION100
2.87-3.290.22031460.17331609X-RAY DIFFRACTION100
3.29-4.140.15661460.15641651X-RAY DIFFRACTION100
4.14-35.740.17091600.17111745X-RAY DIFFRACTION99.06
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)
12.392995492710.0999151712096-1.337928934483.34025368461-1.039410911822.81262881267-0.0780041482368-0.2454538991660.08924515171740.03687632532110.0393980669626-0.3602786761310.07496629104170.32227200321-0.001279843505330.2632486155820.02470201600650.007211493372260.304819256404-0.01162583919650.31075846740523.71100717455.82455651485-17.7154143567
21.692033255970.643461702569-1.461476292361.88848584696-0.2900501375581.30459794213-0.03189716711780.09887441449450.155434534048-0.08774477707070.09342985591240.0980820355771-0.0715431507152-0.267795689755-1.53782185509E-50.2409549569870.0150829305082-0.001920489152970.2677231908240.0130242754550.2631613550357.1505359981710.4840665494-15.6239548322
30.195566200770.4045154212430.00538239051190.8369380140710.01101495396570.0002064878238810.062173396012-0.5689025969680.8238332359320.972107103588-0.2507743698030.722961136714-0.669068983786-0.584056599821-0.01235247684940.658242087251-0.005606169664140.003943750500550.8185970938860.04045449678720.680710946372-4.6889160754613.0157870817-19.6036205813
42.464972961360.543300896715-0.4033580734012.16352410354-0.0647740298821.63011306083-0.1864373259510.00196913991345-0.357690407247-0.07191717911820.0418117917537-0.04690775769760.563869878861-0.170835488834-1.41022438763E-50.406797583317-0.04197792534060.05311154944340.243468580350.008335358927770.283192397539.38011546787-6.67075729013-14.2554779144
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 4 through 124 )4 - 1241 - 112
22chain 'A' and (resid 125 through 197 )125 - 197113 - 185
33chain 'A' and (resid 198 through 216 )198 - 216186 - 200
44chain 'A' and (resid 217 through 309 )217 - 309201 - 293

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