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- PDB-3nr0: Optimization of the in silico designed Kemp eliminase KE70 by com... -

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Basic information

Entry
Database: PDB / ID: 3nr0
TitleOptimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R6 6/10A
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: 2.19 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 30, 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)57,6082
Polymers57,6082
Non-polymers00
Water1,18966
1
A: deoxyribose phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)28,8041
Polymers28,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: deoxyribose phosphate aldolase


Theoretical massNumber of molelcules
Total (without water)28,8041
Polymers28,8041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.105, 41.217, 139.438
Angle α, β, γ (deg.)90.00, 94.96, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein deoxyribose phosphate aldolase


Mass: 28803.760 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.: 66 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE WILD TYPE HAS BEEN ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. THE WILD TYPE HAS BEEN DEPOSITED TO PDB, 3NPU AND 3NPV. THIS SEQUENCE IS ALA 2, SER 19A, ALA 239 INSERTION AND K28N, T42N, Y47F, W71C, G100S, S137A, H165N, A203V MUTANT. ALSO ASP RESIDUE BETWEEN THR 3 AND LEU 4 HAS BEEN DELETION.

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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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2M MgCl2, 0.1M NaAc, 20% PEG 6000, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 9, 2008 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.19→50 Å / Num. all: 29029 / Num. obs: 27694 / % possible obs: 95.4 % / Redundancy: 4 % / Biso Wilson estimate: 31.4 Å2 / Rmerge(I) obs: 0.098 / Rsym value: 0.073 / Net I/σ(I): 15.5
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.08 / Num. unique all: 1383 / Rsym value: 0.43 / % possible all: 95.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0067refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NPU

3npu


Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 6.321 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26838 1416 5.1 %RANDOM
Rwork0.20682 ---
obs0.20993 26268 94.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.412 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å20.42 Å2
2--2.8 Å20 Å2
3----1.58 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3610 0 0 66 3676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223696
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0821.9675010
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.6095486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49624.143140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74415624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5631522
X-RAY DIFFRACTIONr_chiral_restr0.1410.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212712
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_it1.1191.52428
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.00923876
X-RAY DIFFRACTIONr_scbond_it3.65131268
X-RAY DIFFRACTIONr_scangle_it5.8174.51134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.247 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 106 -
Rwork0.253 1791 -
obs--89.19 %

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