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

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Basic information

Entry
Database: PDB / ID: 7riz
TitleCrystal structure of RPA3624, a beta-propeller lactonase from Rhodopseudomonas palustris, with active-site bound 2-hydroxyquinoline
ComponentsBeta-propeller lactonase
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 / QUINOLIN-2(1H)-ONE / Possible gluconolactonase
Function and homology information
Biological speciesRhodopseudomonas palustris (phototrophic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Beta-propeller lactonase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1244
Polymers32,9161
Non-polymers2083
Water3,639202
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.558, 48.558, 199.122
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-538-

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-OCH / QUINOLIN-2(1H)-ONE / 2-OXOQUINOLINE / 2-Quinolone


Mass: 145.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H7NO / 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 / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 2.06 Å3/Da / Density % sol: 40.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystals were grown in a MRC SD2 plate set with a TTP Labtech Mosquito crystallization robot. Protein sample at 9.2mg/mL was inclubated with 5mM 2-hydroxyquinoline at 293K for 1 hour prior ...Details: Crystals were grown in a MRC SD2 plate set with a TTP Labtech Mosquito crystallization robot. Protein sample at 9.2mg/mL was inclubated with 5mM 2-hydroxyquinoline at 293K for 1 hour prior to plate setup. The crystal providing the refinement data set was grown by mixing 200 nL protein-2HQ solution with 100 nL reservoir solution, 24% PEG3350, 0.2 M CaCl2, 0.1M bistris pH 6.5. Crystals were cryoprotected by soaking in reservoir solution supplemented to 30% PEG3350 and direct 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: 1.12723 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 25, 2020
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12723 Å / Relative weight: 1
ReflectionResolution: 1.71→33.19 Å / Num. obs: 30590 / % possible obs: 99.31 % / Redundancy: 19.5 % / Biso Wilson estimate: 27.74 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1008 / Rpim(I) all: 0.02366 / Rrim(I) all: 0.1036 / Net I/σ(I): 17.31
Reflection shellResolution: 1.71→1.771 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.421 / Mean I/σ(I) obs: 1.65 / Num. unique obs: 2983 / CC1/2: 0.964 / CC star: 0.991 / Rpim(I) all: 0.323 / Rrim(I) all: 1.458 / % possible all: 98.19

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7RIS

7ris


Resolution: 1.71→33.19 Å / SU ML: 0.2374 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.785
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2096 1995 6.54 %
Rwork0.1773 28528 -
obs0.1794 30523 99.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.04 Å2
Refinement stepCycle: LAST / Resolution: 1.71→33.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2288 0 13 202 2503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172365
X-RAY DIFFRACTIONf_angle_d1.02973218
X-RAY DIFFRACTIONf_chiral_restr0.0695348
X-RAY DIFFRACTIONf_plane_restr0.0101427
X-RAY DIFFRACTIONf_dihedral_angle_d13.3142866
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.750.36271370.32851955X-RAY DIFFRACTION96.9
1.75-1.80.34521390.30451989X-RAY DIFFRACTION98.06
1.8-1.850.35451370.26971957X-RAY DIFFRACTION98.68
1.85-1.910.30111380.2332008X-RAY DIFFRACTION98.71
1.91-1.980.281390.21831965X-RAY DIFFRACTION98.09
1.98-2.060.24581430.192011X-RAY DIFFRACTION99.22
2.06-2.150.24671410.19672004X-RAY DIFFRACTION99.49
2.15-2.260.22951420.17532038X-RAY DIFFRACTION99.68
2.26-2.410.22651440.18352036X-RAY DIFFRACTION99.95
2.41-2.590.23291430.1752045X-RAY DIFFRACTION99.91
2.59-2.850.20911450.19282092X-RAY DIFFRACTION100
2.85-3.260.19911410.17192069X-RAY DIFFRACTION99.86
3.26-4.110.18561510.16522095X-RAY DIFFRACTION99.91
4.11-33.190.16091550.14632264X-RAY DIFFRACTION99.96
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)
11.336513929420.196686364341-0.5243884091961.38275761803-1.01710524992.557751274730.04506580699290.002545061993710.123099767803-0.0354369918946-0.03091914399070.0731325978299-0.2588190886850.184862888686-0.0003286642939260.25632831586-0.0209505899129-0.01788200074430.256108128522-0.01576366561670.26604688185-19.84329623689.2493000628215.8156332627
20.1677177917210.08075315965680.08811052592430.05548983249260.007622837629390.1030697291550.385879228726-0.526021678997-0.5623611651230.124449925559-0.272864372723-0.03145872200550.834621718419-0.0905135617945-0.001805057406940.6123320867480.06120475938770.002727873654140.6145987303060.05863364541870.469597432428-11.6393524125-11.4161430820.4218928375
31.004717564730.1265596454110.2024274249891.08603178538-0.33872837160.863155256519-0.006816070433230.07231783306420.06545635175590.00158147816165-0.204810129913-0.16763621228-0.3798962972410.797639230393-0.005298859022560.292816554502-0.110579236382-0.003672088561070.5914564479570.06225313168660.323898605514-3.7023650002610.389072564117.4459370851
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 197 )4 - 1971 - 194
22chain 'A' and (resid 198 through 221 )198 - 221195 - 218
33chain 'A' and (resid 222 through 309 )222 - 309219 - 306

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