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- PDB-8foq: Crystal Structure of Kemp Eliminase 1A53-core with bound transiti... -

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Basic information

Entry
Database: PDB / ID: 8foq
TitleCrystal Structure of Kemp Eliminase 1A53-core with bound transition state analogue
ComponentsKemp Eliminase 1A53-core
KeywordsLYASE / Isomerase
Function / homology5-nitro-1H-benzotriazole / PHOSPHATE ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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 1A53-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

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Assembly

Deposited unit
A: Kemp Eliminase 1A53-core
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1873
Polymers29,9281
Non-polymers2592
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area250 Å2
ΔGint-8 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.003, 61.003, 121.977
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

#1: Protein Kemp Eliminase 1A53-core


Mass: 29928.355 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 Gold DE3
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-3NY / 5-nitro-1H-benzotriazole


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.: 169 / 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: 2.239927 Å3/Da / Density % sol: 45.1216 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 10 mM MES, pH 6, 40% v/v PEG400, 5% w/v PEG3000

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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: Sep 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.6→48.48 Å / Num. obs: 34679 / % possible obs: 98.4 % / Redundancy: 8.25 % / Biso Wilson estimate: 24.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.019 / Rrim(I) all: 0.058 / Net I/σ(I): 18.7
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.133 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 1446 / CC1/2: 0.403 / Rpim(I) all: 0.803 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Coot1.17.1_3660model building
XDSdata reduction
PHASERphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→48.48 Å / SU ML: 0.189 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.375
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1859 1659 4.79 %
Rwork0.1592 32962 -
obs0.1604 34621 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.02 Å2
Refinement stepCycle: LAST / Resolution: 1.6→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2013 0 5 169 2187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212179
X-RAY DIFFRACTIONf_angle_d1.1792954
X-RAY DIFFRACTIONf_chiral_restr0.0655325
X-RAY DIFFRACTIONf_plane_restr0.0069384
X-RAY DIFFRACTIONf_dihedral_angle_d15.0305859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.32631240.31222397X-RAY DIFFRACTION87.84
1.65-1.70.29231460.26572575X-RAY DIFFRACTION93.99
1.7-1.760.28121540.23122617X-RAY DIFFRACTION97.09
1.76-1.830.28641200.20692827X-RAY DIFFRACTION99.86
1.84-1.920.23341610.17862711X-RAY DIFFRACTION99.83
1.92-2.020.2191040.16172810X-RAY DIFFRACTION100
2.02-2.150.18231320.152781X-RAY DIFFRACTION100
2.15-2.310.16751460.14522791X-RAY DIFFRACTION99.97
2.31-2.540.15721330.14222795X-RAY DIFFRACTION100
2.55-2.910.18611240.14852824X-RAY DIFFRACTION99.97
2.91-3.670.17071650.14672848X-RAY DIFFRACTION100
3.67-48.480.16721500.15412986X-RAY DIFFRACTION99.97

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