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- PDB-7qjn: Crystal structure of an alpha/beta-hydrolase enzyme from Candidat... -

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Basic information

Entry
Database: PDB / ID: 7qjn
TitleCrystal structure of an alpha/beta-hydrolase enzyme from Candidatus Kryptobacter tengchongensis (306)
ComponentsDienelactone hydrolase
KeywordsHYDROLASE / plastic degradation
Function / homology
Function and homology information


Dienelactone hydrolase / Dienelactone hydrolase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dienelactone hydrolase
Similarity search - Component
Biological speciesCandidatus Kryptobacter tengchongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.885 Å
AuthorsZahn, M. / Gill, R.S. / Erickson, E. / Beckham, G.T. / McGeehan, J.E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)Research England E3 funding United Kingdom
CitationJournal: Nat Commun / Year: 2022
Title: Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity
Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / ...Authors: Erickson, E. / Gado, J.E. / Avilan, L. / Bratti, F. / Brizendine, R.K. / Cox, P.A. / Gill, R. / Graham, R. / Kim, D.J. / Konig, G. / Michener, W.E. / Poudel, S. / Ramirez, K.J. / Shakespeare, T.J. / Zahn, M. / Boyd, E.S. / Payne, C.M. / DuBois, J.L. / Pickford, A.R. / Beckham, G.T. / McGeehan, J.E.
History
DepositionDec 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 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

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Assembly

Deposited unit
A: Dienelactone hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4214
Polymers33,1361
Non-polymers2853
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-19 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.92, 74.92, 116.515
Angle α, β, γ (deg.)90, 90, 120
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-466-

HOH

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Components

#1: Protein Dienelactone hydrolase / alpha/beta-hydrolase


Mass: 33135.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: alpha/beta-hydrolase
Source: (gene. exp.) Candidatus Kryptobacter tengchongensis (bacteria)
Gene: JGI24_00892 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A656D8B6
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.85 Å3/Da / Density % sol: 56.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.8 M sodium phosphate monobasic monohydrate / potassium phosphate dibasic pH 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.89→64.88 Å / Num. obs: 14490 / % possible obs: 93.7 % / Redundancy: 17.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.033 / Net I/σ(I): 14.8
Reflection shellResolution: 1.89→2.12 Å / Rmerge(I) obs: 1.841 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 724 / CC1/2: 0.634 / Rpim(I) all: 0.465

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
autoPROCdata reduction
STARANISOdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: alphafold model

Resolution: 1.885→56.69 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.336 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.347 / SU Rfree Blow DPI: 0.244 / SU Rfree Cruickshank DPI: 0.244
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 663 -RANDOM
Rwork0.2045 ---
obs0.2065 14489 46.5 %-
Displacement parametersBiso mean: 41.34 Å2
Baniso -1Baniso -2Baniso -3
1-5.8228 Å20 Å20 Å2
2--5.8228 Å20 Å2
3----11.6457 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 1.885→56.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2216 0 15 108 2339
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082276HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.973074HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d792SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes380HARMONIC5
X-RAY DIFFRACTIONt_it2276HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion297SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact1918SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.97
X-RAY DIFFRACTIONt_other_torsion18.54
LS refinement shellResolution: 1.89→2.05 Å
RfactorNum. reflection% reflection
Rfree0.3943 18 -
Rwork0.2943 --
obs0.2984 440 6.44 %
Refinement TLS params.Origin x: -3.9748 Å / Origin y: -32.1109 Å / Origin z: -11.6147 Å
111213212223313233
T-0.0145 Å20.0619 Å20.0532 Å2-0.0201 Å20.0388 Å2---0.2231 Å2
L1.3011 °2-0.1688 °20.8619 °2-1.3716 °20.7122 °2--3.758 °2
S0.1443 Å °-0.132 Å °0.2076 Å °-0.132 Å °-0.2163 Å °0.3402 Å °0.2076 Å °0.3402 Å °0.072 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 283
2X-RAY DIFFRACTION1{ A|* }A301 - 304

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