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- PDB-8fos: Crystal Structure of Kemp Eliminase HG3-shell with bound transiti... -

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Basic information

Entry
Database: PDB / ID: 8fos
TitleCrystal Structure of Kemp Eliminase HG3-shell with bound transition state analogue
ComponentsKemp Eliminase HG3-shell
KeywordsLYASE / Artificial enzyme
Function / homology6-NITROBENZOTRIAZOLE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsZarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04831 Canada
Canada Foundation for Innovation26503 Canada
CitationJournal: To Be Published
Title: Crystal Structure of Kemp Eliminase HG3-shell with bound transition state analogue
Authors: Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A.
History
DepositionJan 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kemp Eliminase HG3-shell
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0043
Polymers34,6461
Non-polymers3582
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint5 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.908, 66.569, 72.518
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Kemp Eliminase HG3-shell


Mass: 34645.941 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3-Gold
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.64473 Å3/Da / Density % sol: 25.26213 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1% w/v PEG2000 MME, 0.1 M HEPES, pH 7, 1 M sodium succinate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.56→72.52 Å / Num. obs: 27999 / % possible obs: 81.6 % / Redundancy: 6.19 % / Biso Wilson estimate: 17.77 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.043 / Rrim(I) all: 0.109 / Χ2: 1 / Net I/σ(I): 12.9
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 1.3 / Mean I/σ(I) obs: 2 / Num. unique obs: 485 / CC1/2: 0.363 / Rpim(I) all: 0.95 / Rrim(I) all: 1.471 / Χ2: 0.9 / % possible all: 29.7

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Coot1.17.1_3660model building
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→49.04 Å / SU ML: 0.161 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 19.6116
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1817 1414 5.06 %
Rwork0.1573 26542 -
obs0.1585 27956 81.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.91 Å2
Refinement stepCycle: LAST / Resolution: 1.56→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2299 0 13 133 2445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00492502
X-RAY DIFFRACTIONf_angle_d0.72873430
X-RAY DIFFRACTIONf_chiral_restr0.0465374
X-RAY DIFFRACTIONf_plane_restr0.0048457
X-RAY DIFFRACTIONf_dihedral_angle_d13.7564901
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.620.2816610.25051002X-RAY DIFFRACTION31.47
1.62-1.680.2958780.23351396X-RAY DIFFRACTION43.75
1.68-1.760.2605990.22421966X-RAY DIFFRACTION60.56
1.76-1.850.23491620.20292815X-RAY DIFFRACTION87.95
1.85-1.970.20211780.17523122X-RAY DIFFRACTION96.24
1.97-2.120.19441650.15623127X-RAY DIFFRACTION96.85
2.12-2.330.16941570.13213180X-RAY DIFFRACTION97.6
2.33-2.670.1791370.1363268X-RAY DIFFRACTION98.47
2.67-3.360.15721820.14493247X-RAY DIFFRACTION98.45
3.36-49.040.171950.16063419X-RAY DIFFRACTION98.96
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)
11.448935048990.1298233619520.04112713525741.38053460320.6716372433216.74443547853-0.00197927859013-0.00796497159606-0.04716478630060.02137607508150.007734620987590.06982945544710.127839504401-0.0901366451689-0.01022130097030.09059381078680.00105799943729-0.003796645754810.0969575516455-0.007052141017530.1112718843-24.23098183174.17041944789-10.0888300807
29.416560891190.138871018139-3.263354409621.59952195843-0.3886066636162.242393188450.03668301907710.09472475705440.0852003067694-0.1841907175290.0164674656235-0.00345170562844-0.07754087165750.0892023539539-0.05773936675790.171307627283-0.0237454228546-0.02798255655590.13119635007-0.02488934858160.0761007671558-12.454780628412.5953370399-21.8210668606
32.728105506120.170914304687-0.3605838598720.94572230642-0.069125670010.914042280336-0.05950474855480.122634170802-0.0900298717135-0.1247364770940.0420618473067-0.1662831677060.001860202945010.2413917908920.01992484756110.141032895438-0.01768184934960.01401546266010.169184273436-0.02516580431280.0898637204344-1.3149858349112.4683281161-17.4871773468
40.7324862385750.0497405162619-0.1554229230561.2830172199-0.6464296450721.44227993995-0.0339010702628-0.0126953701460.005974279596710.00329582126533-0.02223478463-0.09413146965210.05417002727430.07164529026950.06021442649950.08925614153260.001246110108770.002819911764210.152568543892-0.02021204983090.0869673557938-0.7408759071058.3970065379-7.06397374349
50.7854176930271.427378793130.9766381442946.897759763292.668912565182.029453037160.00252994631846-0.0652736764879-0.1036487565990.3480679307030.0730081892938-0.444411391620.1053184892870.0999799040609-0.0718022542540.09328602449440.000581970897157-0.0005551287667620.1478544186480.006358504411530.1241828405313.328351000155.232884622383.21365949426
61.243658170530.8955872541190.4775926758412.030153081150.03118137010470.735596845671-0.02388657099040.0120903251494-0.134700638361-0.0560553533260.05465278017370.01114438706080.05286982494460.0175199804351-0.02727346589270.1363452452070.01517486045630.01472230213160.1674883386-0.003987660739910.130895718447-9.20913810963-0.484372089415-0.543634917258
72.122200539930.7839501279610.8962404540052.2915123740.632904163722.434902261060.08202963678580.0307467392637-0.135977926741-0.08930979526530.00995881586040.05571100343670.215088631031-0.0657996796136-0.07359418575850.1384902849960.007345361867830.0001908054298060.1339166203240.003502274317730.137202787869-21.4964956624-5.46039546619-5.30096422692
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 45 )
2X-RAY DIFFRACTION2chain 'A' and (resid 46 through 76 )
3X-RAY DIFFRACTION3chain 'A' and (resid 77 through 119 )
4X-RAY DIFFRACTION4chain 'A' and (resid 120 through 181 )
5X-RAY DIFFRACTION5chain 'A' and (resid 182 through 196 )
6X-RAY DIFFRACTION6chain 'A' and (resid 197 through 244 )
7X-RAY DIFFRACTION7chain 'A' and (resid 245 through 302 )

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