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- PDB-3uy8: Designed protein KE59 R5_11/5F -

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Basic information

Entry
Database: PDB / ID: 3uy8
TitleDesigned protein KE59 R5_11/5F
ComponentsKemp eliminase KE59 R5_11/5F
KeywordsLYASE / Structural Genomics / Israel Structural Proteomics Center / ISPC / Beta Barrel
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsKhersonsky, O. / Kiss, G. / Roethlisberger, D. / Dym, O. / Albeck, S. / Houk, K.N. / Baker, D. / Tawfik, D.S. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59.
Authors: Khersonsky, O. / Kiss, G. / Rothlisberger, D. / Dym, O. / Albeck, S. / Houk, K.N. / Baker, D. / Tawfik, D.S.
History
DepositionDec 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2012Group: Database references
Revision 1.2Jul 11, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Kemp eliminase KE59 R5_11/5F
B: Kemp eliminase KE59 R5_11/5F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9414
Polymers56,7492
Non-polymers1922
Water905
1
A: Kemp eliminase KE59 R5_11/5F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4712
Polymers28,3751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kemp eliminase KE59 R5_11/5F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4712
Polymers28,3751
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.961, 102.727, 66.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Kemp eliminase KE59 R5_11/5F


Mass: 28374.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: Lyases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 5.5, 25% PEG3350, 0.01 M magnesium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 10, 2009
Details: Pt coated mirrors in Kirkpatrick-Baez (KB) geometry
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.4→43.98 Å / Num. all: 23939 / Num. obs: 23532 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rmerge(I) obs: 0.073 / Rsym value: 0.057 / Net I/σ(I): 28.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.424 / % possible all: 87.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UYC

3uyc


Resolution: 2.41→43.98 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.189 / SU ML: 0.218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.421 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.29897 1201 5.1 %RANDOM
Rwork0.21466 ---
obs0.21884 22286 98.21 %-
all-22692 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20 Å2
2--1.86 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.41→43.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3932 0 10 5 3947
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0370.0224049
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.7821.995457
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7865491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.54523.83188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.22515788
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8571538
X-RAY DIFFRACTIONr_chiral_restr0.2060.2621
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212968
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5881.52459
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.8323992
X-RAY DIFFRACTIONr_scbond_it4.54731590
X-RAY DIFFRACTIONr_scangle_it7.084.51465
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 89 -
Rwork0.27 1433 -
obs--87.98 %

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