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- PDB-8fmc: Crystal Structure of Kemp Eliminase 1A53-core in unbound state -

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Basic information

Entry
Database: PDB / ID: 8fmc
TitleCrystal Structure of Kemp Eliminase 1A53-core in unbound state
ComponentsKemp Eliminase 1A53-core
KeywordsLYASE / Artificial enzyme
Function / homologyPHOSPHATE ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 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 in unbound state
Authors: Zarifi, N. / Asthana, P. / Fraser, J.S. / Chica, R.A.
History
DepositionDec 23, 2022Deposition 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)30,2193
Polymers29,9281
Non-polymers2902
Water77543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area720 Å2
ΔGint-1 kcal/mol
Surface area10990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.687, 60.687, 121.762
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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.212837 Å3/Da / Density % sol: 44.44978 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1 M 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 S 6M / Detector: PIXEL / Date: Nov 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.36→52.56 Å / Num. obs: 11245 / % possible obs: 99.96 % / Redundancy: 9.47 % / Biso Wilson estimate: 35.48 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.129 / Rpim(I) all: 0.044 / Rrim(I) all: 0.137 / Χ2: 0.99 / Net I/σ(I): 11.9
Reflection shellResolution: 2.36→2.45 Å / Rmerge(I) obs: 0.522 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 1152 / CC1/2: 0.932 / Rpim(I) all: 0.174 / Rrim(I) all: 0.551 / Χ2: 0.99 / % possible all: 100

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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
Starting model: PDB entry 6NW4

6nw4


Resolution: 2.36→52.56 Å / SU ML: 0.2409 / Cross valid method: FREE R-VALUE / σ(F): 1.93 / Phase error: 22.6466
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2314 595 5.31 %
Rwork0.1907 10613 -
obs0.1928 11208 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.14 Å2
Refinement stepCycle: LAST / Resolution: 2.36→52.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1995 0 17 43 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332077
X-RAY DIFFRACTIONf_angle_d0.52662804
X-RAY DIFFRACTIONf_chiral_restr0.0447312
X-RAY DIFFRACTIONf_plane_restr0.0028358
X-RAY DIFFRACTIONf_dihedral_angle_d16.8684814
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.60.28351520.20672581X-RAY DIFFRACTION100
2.6-2.970.2541560.20982604X-RAY DIFFRACTION99.96
2.97-3.740.23031400.19122649X-RAY DIFFRACTION100
3.75-52.560.20841470.18032779X-RAY DIFFRACTION99.9

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