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- PDB-8for: Crystal Structure of Kemp Eliminase KE70-core with bound transiti... -

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Basic information

Entry
Database: PDB / ID: 8for
TitleCrystal Structure of Kemp Eliminase KE70-core with bound transition state analogue
ComponentsKemp Eliminase KE70-core
KeywordsLYASE / Artificial enzyme
Function / homology6-NITROBENZOTRIAZOLE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 KE70-core 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kemp Eliminase KE70-core
B: Kemp Eliminase KE70-core
C: Kemp Eliminase KE70-core
D: Kemp Eliminase KE70-core
E: Kemp Eliminase KE70-core
F: Kemp Eliminase KE70-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,29712
Polymers172,3126
Non-polymers9856
Water3,711206
1
A: Kemp Eliminase KE70-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8832
Polymers28,7191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Kemp Eliminase KE70-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8832
Polymers28,7191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Kemp Eliminase KE70-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8832
Polymers28,7191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Kemp Eliminase KE70-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8832
Polymers28,7191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Kemp Eliminase KE70-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8832
Polymers28,7191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Kemp Eliminase KE70-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8832
Polymers28,7191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.789, 155.642, 190.588
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 KE70-core


Mass: 28718.650 Da / Num. of mol.: 6
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-6NT / 6-NITROBENZOTRIAZOLE


Mass: 164.122 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H4N4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.14802 Å3/Da / Density % sol: 42.77353 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M HEPES, pH 8.5, 20% PEG4000

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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 6M / Detector: PIXEL / Date: Mar 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.2→39.71 Å / Num. obs: 80798 / % possible obs: 99.9 % / Redundancy: 6.77 % / Biso Wilson estimate: 36.24 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.089 / Rrim(I) all: 0.234 / Χ2: 1 / Net I/σ(I): 6.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 2.288 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 4495 / CC1/2: 0.497 / Rpim(I) all: 0.925 / Χ2: 0.99 / % possible all: 100

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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
Starting model: PDB entry 8FMD

8fmd


Resolution: 2.2→39.71 Å / SU ML: 0.2981 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 25.5469
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2363 4078 5.05 %
Rwork0.2085 76630 -
obs0.2099 80708 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.53 Å2
Refinement stepCycle: LAST / Resolution: 2.2→39.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11107 0 0 206 11313
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001911383
X-RAY DIFFRACTIONf_angle_d0.466515454
X-RAY DIFFRACTIONf_chiral_restr0.03871841
X-RAY DIFFRACTIONf_plane_restr0.00291997
X-RAY DIFFRACTIONf_dihedral_angle_d12.63184076
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.34661280.32592576X-RAY DIFFRACTION100
2.23-2.250.33361380.322605X-RAY DIFFRACTION99.96
2.25-2.280.35961370.30462617X-RAY DIFFRACTION100
2.28-2.310.34071260.30232615X-RAY DIFFRACTION100
2.31-2.340.33151260.29632612X-RAY DIFFRACTION100
2.34-2.380.31751420.28942615X-RAY DIFFRACTION100
2.38-2.410.33811260.27812660X-RAY DIFFRACTION99.93
2.41-2.450.27351490.2662565X-RAY DIFFRACTION99.85
2.45-2.490.33411320.25562616X-RAY DIFFRACTION99.89
2.49-2.530.321460.26082629X-RAY DIFFRACTION99.96
2.53-2.580.2691290.25292594X-RAY DIFFRACTION99.96
2.58-2.630.26061290.2522653X-RAY DIFFRACTION99.96
2.63-2.680.26911570.24142597X-RAY DIFFRACTION99.85
2.68-2.740.30871470.24362616X-RAY DIFFRACTION99.93
2.74-2.80.29941480.25442610X-RAY DIFFRACTION99.64
2.8-2.870.31911460.25142607X-RAY DIFFRACTION99.75
2.87-2.950.30551460.24792655X-RAY DIFFRACTION100
2.95-3.040.3011250.24042642X-RAY DIFFRACTION99.93
3.04-3.140.26721510.23212614X-RAY DIFFRACTION99.86
3.14-3.250.26461370.23342629X-RAY DIFFRACTION99.96
3.25-3.380.27131430.22362646X-RAY DIFFRACTION100
3.38-3.530.22351230.22322703X-RAY DIFFRACTION100
3.53-3.720.19241330.18252654X-RAY DIFFRACTION99.93
3.72-3.950.19691510.16722627X-RAY DIFFRACTION99.78
3.95-4.260.1811440.15862680X-RAY DIFFRACTION99.68
4.26-4.680.17021410.14112697X-RAY DIFFRACTION99.93
4.68-5.360.1681700.14612695X-RAY DIFFRACTION99.93
5.36-6.750.20131440.18162728X-RAY DIFFRACTION99.83
6.75-39.710.17541640.15962873X-RAY DIFFRACTION99.64

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