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- PDB-3q2d: Optimization of the in silico designed Kemp eliminase KE70 by com... -

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Basic information

Entry
Database: PDB / ID: 3q2d
TitleOptimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution
ComponentsDeoxyribose phosphate aldolase
KeywordsLYASE / Structural Genomics / Israel Structural Proteomics Center / ISPC / TIM
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 5-nitro-1H-benzotriazole
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. / Murphy, P. / Dym, O. / Albeck, S. / Kiss, G. / Houk, K.N. / 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
DepositionDec 20, 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 ...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: Deoxyribose phosphate aldolase
B: Deoxyribose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1664
Polymers57,8382
Non-polymers3282
Water61334
1
A: Deoxyribose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0832
Polymers28,9191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Deoxyribose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0832
Polymers28,9191
Non-polymers1641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.837, 41.307, 138.781
Angle α, β, γ (deg.)90.00, 95.36, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Deoxyribose phosphate aldolase


Mass: 28918.850 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: Chemical ChemComp-3NY / 5-nitro-1H-benzotriazole


Mass: 164.122 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H4N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M NaMalonate, Imidazole, Boric acid pH4, 25% PEG 1500 , pH 4.6, 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: Aug 20, 2010
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: 28757 / Num. obs: 27722 / % possible obs: 96.4 % / Redundancy: 4.6 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 15.1
Reflection shellResolution: 2.19→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.342 / % possible all: 79.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NRQ

3nrq


Resolution: 2.19→50 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.901 / SU B: 5.942 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R Free: 0.229
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27223 1403 5.1 %RANDOM
Rwork0.21804 ---
obs0.22072 26309 95.92 %-
all-28757 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.622 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20.46 Å2
2--3.33 Å20 Å2
3----2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3454 0 24 34 3512
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0223667
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.9724981
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955488
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45624.341129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.22315590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9861518
X-RAY DIFFRACTIONr_chiral_restr0.1280.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212696
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_it1.0921.52438
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9323887
X-RAY DIFFRACTIONr_scbond_it3.46131229
X-RAY DIFFRACTIONr_scangle_it5.1954.51094
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
Rfree0.48 79 -
Rwork0.289 1510 -
obs--75.81 %

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