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- PDB-7qjm: Crystal structure of an alpha/beta-hydrolase enzyme from Chlorofl... -

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Basic information

Entry
Database: PDB / ID: 7qjm
TitleCrystal structure of an alpha/beta-hydrolase enzyme from Chloroflexus sp. MS-G (202)
Componentsalpha/beta-hydrolase (202)
KeywordsHYDROLASE / plastic degradation / peptidase
Biological speciesChloroflexus sp. MS-G (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsZahn, M. / Graham, R. / 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 1.1Jan 31, 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: alpha/beta-hydrolase (202)
B: alpha/beta-hydrolase (202)


Theoretical massNumber of molelcules
Total (without water)84,6472
Polymers84,6472
Non-polymers00
Water2,504139
1
A: alpha/beta-hydrolase (202)


Theoretical massNumber of molelcules
Total (without water)42,3231
Polymers42,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: alpha/beta-hydrolase (202)


Theoretical massNumber of molelcules
Total (without water)42,3231
Polymers42,3231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.68, 124.91, 169.99
Angle α, β, γ (deg.)90, 90, 90
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-407-

HOH

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Components

#1: Protein alpha/beta-hydrolase (202)


Mass: 42323.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus sp. MS-G (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 15 % PEG 3350, 0.1 M succinic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.19→50.33 Å / Num. obs: 49979 / % possible obs: 100 % / Redundancy: 13.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.026 / Net I/σ(I): 14.6
Reflection shellResolution: 2.19→2.23 Å / Redundancy: 13.5 % / Rmerge(I) obs: 3.181 / Mean I/σ(I) obs: 0.9 / Num. unique obs: 2460 / CC1/2: 0.292 / Rpim(I) all: 0.893 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7d78

7d78


Resolution: 2.19→50.33 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU R Cruickshank DPI: 0.185 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.182 / SU Rfree Blow DPI: 0.162 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.2442 2537 -RANDOM
Rwork0.2158 ---
obs0.2172 49979 100 %-
Displacement parametersBiso mean: 79.76 Å2
Baniso -1Baniso -2Baniso -3
1-3.5838 Å20 Å20 Å2
2--0.5005 Å20 Å2
3----4.0842 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.19→50.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4629 0 0 139 4768
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084736HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.976452HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1611SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes802HARMONIC5
X-RAY DIFFRACTIONt_it4736HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion604SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3802SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion17.54
LS refinement shellResolution: 2.19→2.21 Å
RfactorNum. reflection% reflection
Rfree0.3464 50 -
Rwork0.3833 --
obs0.3815 1000 100 %
Refinement TLS params.

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)
12.91440.50121.08580.70220.93592.6189-0.1655-0.07560.0122-0.07560.1090.2230.01220.2230.05640.0344-0.0184-0.12980.01540.0793-0.056714.1544-33.707317.6131
22.3870.9996-0.16582.91262.06962.9522-0.1563-0.3097-0.1802-0.3097-0.2441-0.7702-0.1802-0.77020.4004-0.0752-0.0207-0.08990.11610.02410.2169-13.6795-18.536730.8241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A77 - 377
2X-RAY DIFFRACTION2{ B|* }B80 - 376

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