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- PDB-7mqx: P. putida mandelate racemase forms an oxobenzoxaborole adduct wit... -

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Basic information

Entry
Database: PDB / ID: 7mqx
TitleP. putida mandelate racemase forms an oxobenzoxaborole adduct with 2-formylphenylboronic acid
ComponentsMandelate racemase
KeywordsISOMERASE/ISOMERASE INHIBITOR / Boronate / ISOMERASE / ISOMERASE-INHIBITOR complex / ISOMERASE-ISOMERASE INHIBITOR complex
Function / homology
Function and homology information


mandelate racemase / mandelate racemase activity / mandelate catabolic process / amino acid catabolic process / hydro-lyase activity / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like ...Mandelate racemase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily
Similarity search - Domain/homology
(3S)-2,1-benzoxaborole-1,3(3H)-diol / Mandelate racemase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.914 Å
AuthorsGrandinetti, L. / Bearne, S.L. / St.Maurice, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-05083 Canada
CitationJournal: Biochemistry / Year: 2021
Title: Slow-Onset, Potent Inhibition of Mandelate Racemase by 2-Formylphenylboronic Acid. An Unexpected Adduct Clasps the Catalytic Machinery.
Authors: Douglas, C.D. / Grandinetti, L. / Easton, N.M. / Kuehm, O.P. / Hayden, J.A. / Hamilton, M.C. / St Maurice, M. / Bearne, S.L.
History
DepositionMay 6, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 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: Mandelate racemase
B: Mandelate racemase
C: Mandelate racemase
D: Mandelate racemase
E: Mandelate racemase
F: Mandelate racemase
G: Mandelate racemase
H: Mandelate racemase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)333,32148
Polymers330,4378
Non-polymers2,88440
Water38,7862153
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: the homooctamer is the well-established oligomerization state of this enzyme
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32100 Å2
ΔGint-61 kcal/mol
Surface area81380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)225.483, 149.430, 149.523
Angle α, β, γ (deg.)90.000, 129.340, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Mandelate racemase / MR


Mass: 41304.621 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: mdlA / Production host: Escherichia coli (E. coli) / References: UniProt: P11444, mandelate racemase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ZMD / (3S)-2,1-benzoxaborole-1,3(3H)-diol


Mass: 149.940 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C7H7BO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2153 / 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: 2.97 Å3/Da / Density % sol: 58.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Reservoir solution: PEG 3350 (3% w/v), Bis-Tris Propane (50 mM) Protein solution:P. putida mandelate racemase (6 mg/mL), 2-formylphenylboronic acid (1.0 mM), MgCl2 (3.3 mM), and Na+-HEPES ...Details: Reservoir solution: PEG 3350 (3% w/v), Bis-Tris Propane (50 mM) Protein solution:P. putida mandelate racemase (6 mg/mL), 2-formylphenylboronic acid (1.0 mM), MgCl2 (3.3 mM), and Na+-HEPES buffer (50 mM, pH 7.5) The protein solution and reservoir solution were mixed in a 1:1 ratio to a final volume of 10 microliters

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12709 Å
DetectorType: DECTRIS EIGER X 9M / Detector: CCD / Date: Aug 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12709 Å / Relative weight: 1
ReflectionResolution: 1.91→113.47 Å / Num. obs: 291736 / % possible obs: 99.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 20.15 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.078 / Rrim(I) all: 0.203 / Net I/σ(I): 7.9
Reflection shellResolution: 1.914→1.947 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.012 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 14397 / CC1/2: 0.721 / Rpim(I) all: 0.42 / Rrim(I) all: 1.099 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å113.47 Å
Translation2.5 Å113.47 Å

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UXK

3uxk


Resolution: 1.914→40.606 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2147 14797 5.08 %
Rwork0.1872 276706 -
obs0.1886 291503 99.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.22 Å2 / Biso mean: 21.3997 Å2 / Biso min: 8.53 Å2
Refinement stepCycle: final / Resolution: 1.914→40.606 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21487 0 192 2153 23832
Biso mean--23.64 27.62 -
Num. residues----2857
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9142-1.9360.27784550.2571905998
1.936-1.95870.28624820.24259295100
1.9587-1.98260.30224810.24649254100
1.9826-2.00770.26584740.22589233100
2.0077-2.03410.26154700.21049271100
2.0341-2.0620.25924880.20129227100
2.062-2.09150.24834470.19669352100
2.0915-2.12270.25795040.20279216100
2.1227-2.15580.26514710.19899279100
2.1558-2.19120.2565020.29254100
2.1912-2.2290.2294860.19329279100
2.229-2.26950.21634870.18929260100
2.2695-2.31310.2455150.19239197100
2.3131-2.36030.24075240.19179216100
2.3603-2.41170.24815550.1983920699
2.4117-2.46780.22445640.1871911499
2.4678-2.52950.22685370.1858921699
2.5295-2.59780.24144520.1951916599
2.5978-2.67430.22034550.1908873094
2.6743-2.76060.22075170.18779205100
2.7606-2.85920.22285640.19089206100
2.8592-2.97370.20214870.18089271100
2.9737-3.10890.22044320.18959373100
3.1089-3.27280.21814630.19419305100
3.2728-3.47770.2125010.18639333100
3.4777-3.74610.18064960.1737923199
3.7461-4.12270.17274690.1663926499
4.1227-4.71850.16674940.1679918099
4.7185-5.94190.185180.1767908797
5.9419-40.6060.18915070.16159428100

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