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- PDB-8usi: Crystal Structure of Kemp Eliminase HG198 in unbound state, 280 K -

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Basic information

Entry
Database: PDB / ID: 8usi
TitleCrystal Structure of Kemp Eliminase HG198 in unbound state, 280 K
ComponentsKemp eliminase
KeywordsHYDROLASE / De novo enzyme design / computational protein design / Kemp eliminases / biocatalysis / directed evolution / X-ray crystallography
Biological speciesThermoascus aurantiacus (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeifinoferest, B.
Funding support Canada, France, United States, 4items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canada Foundation for Innovation Canada
Human Frontier Science Program (HFSP) France
Department of Energy (DOE, United States) United States
CitationJournal: J.Am.Chem.Soc. / Year: 2024
Title: Design of Efficient Artificial Enzymes Using Crystallographically Enhanced Conformational Sampling.
Authors: Rakotoharisoa, R.V. / Seifinoferest, B. / Zarifi, N. / Miller, J.D.M. / Rodriguez, J.M. / Thompson, M.C. / Chica, R.A.
History
DepositionOct 27, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kemp eliminase


Theoretical massNumber of molelcules
Total (without water)34,3391
Polymers34,3391
Non-polymers00
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.677, 58.715, 51.301
Angle α, β, γ (deg.)90.000, 95.360, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Kemp eliminase


Mass: 34339.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoascus aurantiacus (fungus) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 6 mg/mL protein, 100 mM sodium acetate, pH 4.6, 1.8 M ammonium sulfate

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Data collection

DiffractionMean temperature: 280 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→58.72 Å / Num. obs: 21360 / % possible obs: 99.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 9.58 Å2 / CC1/2: 0.955 / Rmerge(I) obs: 0.264 / Rpim(I) all: 0.169 / Net I/σ(I): 6
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 1030 / CC1/2: 0.493 / Rpim(I) all: 0.517 / % possible all: 99.6

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Processing

Software
NameVersionClassification
xia20.5.492data reduction
DIALSXia2 0.5.492data reduction
AimlessXia2 0.5.492data scaling
Coot0.8.9.236model building
PHASERv1.13.2998phasing
PHENIXv1.13.2998refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→51.08 Å / SU ML: 0.2246 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.8074
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 1023 4.8 %
Rwork0.1585 20311 -
obs0.1604 21334 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.51 Å2
Refinement stepCycle: LAST / Resolution: 1.9→51.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 0 294 2596
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00292473
X-RAY DIFFRACTIONf_angle_d0.60683397
X-RAY DIFFRACTIONf_chiral_restr0.0429381
X-RAY DIFFRACTIONf_plane_restr0.0038453
X-RAY DIFFRACTIONf_dihedral_angle_d11.7214887
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-20.28271430.24862861X-RAY DIFFRACTION99.6
2-2.130.2441640.21052852X-RAY DIFFRACTION99.7
2.13-2.290.24741440.19052906X-RAY DIFFRACTION99.93
2.29-2.520.23141540.17512890X-RAY DIFFRACTION99.74
2.52-2.880.20121410.16032900X-RAY DIFFRACTION99.77
2.88-3.630.18881360.12942923X-RAY DIFFRACTION99.61
3.63-51.080.1251410.10942979X-RAY DIFFRACTION99.87
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)
13.65074804112.5094421665-1.494391145852.97355391697-1.120906451751.52736216447-0.0383585497376-0.109955255304-0.0150555825427-0.01653827136640.02193070523540.01694811355980.09751320484010.207166471110.03019178513090.08639626195680.0266808672771-0.002354324756570.0929553401693-0.01474559932470.099246867765216.0483338022-12.617677610326.7013068608
20.364735525899-0.01325939981910.5000218978940.138643740709-0.2430369964921.839899483140.04331093634790.0009740835016550.0343099693933-0.0032495367706-0.0176047239325-0.0204295392392-0.01357977216990.104542511577-0.01624108765530.112609782742-0.001421926290090.002526711888470.113269759734-0.00368669832580.12068162624913.861433291-7.102378555389.25011898725
30.526330549832-0.208460022673-0.2154181188330.8542893813-0.7280961181072.119581867330.0400261049185-0.0123918735534-0.00344019891182-0.094571778511-0.0151461782064-0.03057638916230.1579075247970.0933043640754-0.01900276028240.096579797889-0.007042971540150.0003433148756040.100972410805-0.01142704093230.09268610254417.14452576464-13.17536891232.59555133816
40.394801807805-0.264400290075-0.5023312767540.774540975590.3347227121911.38397705442-0.0006407739641250.05109091692130.00980370988745-0.0269414755604-0.01916991753820.00470241522063-0.0358056814535-0.09130485874380.002520494704470.1037324205-0.00527246379191-0.004465038776140.102656971856-0.008224342396240.0961140980774-3.38665009473-8.120241053849.26443499662
50.674148520594-1.09280664322-1.238886887454.348405648552.562430799422.87463408135-0.01019587974010.120848559418-0.05524321553660.0490517360319-0.07502238376630.2066653956880.125897233638-0.1507305708330.1389475230080.0880947066811-0.0190258082358-0.03647958510130.149696360835-0.006958156932460.125636164248-11.6100002934-11.036198595814.492100809
60.7190623319660.5652661190440.3105955252490.7295596315040.6772649923770.9977594540330.00824764320074-0.03285087407210.01238542457880.0283826994697-0.01595156396040.01279245985460.028768260698-0.01940912001910.009524319391450.09710185701030.001562665759710.006877600717040.08347246785590.0009664018232070.1011550493310.946333226144-8.736028230125.7259380246
72.750867675710.365917533839-0.7997966045883.24686089146-0.1647277373891.471892229380.1161508882580.03845460507180.188142443810.00506107906294-0.140871224521-0.170333892633-0.1276769857470.192701377333-0.05109630407910.0647056545901-0.00291757760180.01040206680460.14572939228-0.01063785109990.078020684932713.7045269727-1.9462215124232.9026171577
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 31 )
2X-RAY DIFFRACTION2chain 'A' and (resid 32 through 100 )
3X-RAY DIFFRACTION3chain 'A' and (resid 101 through 130 )
4X-RAY DIFFRACTION4chain 'A' and (resid 131 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 270 )
7X-RAY DIFFRACTION7chain 'A' and (resid 271 through 303 )

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