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- PDB-3uy7: Designed protein KE59 R1 7/10H with G130S mutation -

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Basic information

Entry
Database: PDB / ID: 3uy7
TitleDesigned protein KE59 R1 7/10H with G130S mutation
ComponentsKemp eliminase KE59 R1 7/10H
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: 1.45 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 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Database references
Revision 1.2Sep 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

Downloads & links

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Assembly

Deposited unit
A: Kemp eliminase KE59 R1 7/10H
B: Kemp eliminase KE59 R1 7/10H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0859
Polymers57,5592
Non-polymers5267
Water3,495194
1
A: Kemp eliminase KE59 R1 7/10H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1146
Polymers28,7791
Non-polymers3345
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Kemp eliminase KE59 R1 7/10H
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9713
Polymers28,7791
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.529, 61.529, 119.961
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Kemp eliminase KE59 R1 7/10H


Mass: 28779.373 Da / Num. of mol.: 2 / Mutation: G130S
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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG3350, 0.2 M sodium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9197 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 16, 2011
RadiationMonochromator: channel cut Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9197 Å / Relative weight: 1
ReflectionResolution: 1.45→39.987 Å / Num. all: 90264 / Num. obs: 90084 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.067 / Net I/σ(I): 23.5
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.534 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UYC

3uyc


Resolution: 1.45→39.987 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.303 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2035 4510 5 %RANDOM
Rwork0.16276 ---
obs0.16478 85529 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.147 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å2-0.15 Å20 Å2
2---0.3 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 1.45→39.987 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 27 194 4103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0223992
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2162.0055391
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4215498
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23623.735166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.60615778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0051537
X-RAY DIFFRACTIONr_chiral_restr0.1720.2635
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212867
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_it2.7151.52481
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.92924032
X-RAY DIFFRACTIONr_scbond_it6.19831511
X-RAY DIFFRACTIONr_scangle_it8.7714.51358
X-RAY DIFFRACTIONr_rigid_bond_restr2.98433992
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 302 -
Rwork0.195 6176 -
obs--96.61 %

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