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- PDB-3npu: Optimization of the in silico designed Kemp eliminase KE70 by com... -

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Basic information

Entry
Database: PDB / ID: 3npu
TitleOptimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution
Componentsdeoxyribose phosphate aldolase
KeywordsLYASE / TIM / Structural Genomics / Israel Structural Proteomics Center / ISPC
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsKhersonsky, O. / Rothlisberge, D. / Wollacott, A.M. / Dym, O. / Baker, D. / Tawfik, D.S. / Israel Structural Proteomics Center (ISPC)
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution
Authors: Khersonsky, O. / Rothlisberger, D. / Wollacott, A.M. / Murphy, P. / Dym, O. / Albeck, S. / Kiss, G. / Houk, K.N. / Baker, D. / Tawfik, D.S.
History
DepositionJun 29, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: deoxyribose phosphate aldolase
B: deoxyribose phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)55,8882
Polymers55,8882
Non-polymers00
Water73941
1
A: deoxyribose phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)27,9441
Polymers27,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: deoxyribose phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)27,9441
Polymers27,9441
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.222, 53.295, 81.846
Angle α, β, γ (deg.)90.00, 110.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein deoxyribose phosphate aldolase


Mass: 27943.854 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)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 46.03 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M NaF, 0.1M Bis Tris Propane, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 22, 2008 / Details: mirros
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 23599 / % possible obs: 97.8 % / Observed criterion σ(F): 51193 / Redundancy: 6.5 % / Biso Wilson estimate: 30.25 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.077 / Net I/σ(I): 22.28
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2034 / Rsym value: 0.195 / % possible all: 83.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JCJ

1jcj


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.51 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24116 1207 5.1 %RANDOM
Rwork0.18927 ---
obs0.19198 22380 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.257 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-1.22 Å2
2--0.14 Å20 Å2
3----1.8 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3651 0 0 41 3692
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223759
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9655095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.945492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.27224.069145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.89115634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0071522
X-RAY DIFFRACTIONr_chiral_restr0.1220.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022772
X-RAY DIFFRACTIONr_nbd_refined0.1990.21632
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22581
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2180.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.23
X-RAY DIFFRACTIONr_mcbond_it0.9441.52560
X-RAY DIFFRACTIONr_mcangle_it1.51523909
X-RAY DIFFRACTIONr_scbond_it2.67231405
X-RAY DIFFRACTIONr_scangle_it4.1054.51186
LS refinement shellResolution: 2.248→2.306 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 85 -
Rwork0.214 1292 -
obs--76.33 %

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