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- PDB-3nq2: Optimization of the in silico designed Kemp eliminase KE70 by com... -

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Basic information

Entry
Database: PDB / ID: 3nq2
TitleOptimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R2 3/5G
Componentsdeoxyribose phosphate aldolase
KeywordsLYASE / TIM / Structural Genomics / Israel Structural Proteomics Center / ISPC
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / IMIDAZOLE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.02 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 ...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)56,2524
Polymers56,1142
Non-polymers1382
Water2,828157
1
A: deoxyribose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1262
Polymers28,0571
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: deoxyribose phosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1262
Polymers28,0571
Non-polymers691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.008, 96.228, 71.274
Angle α, β, γ (deg.)90.00, 125.88, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein deoxyribose phosphate aldolase


Mass: 28056.967 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-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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 INSERTION AND Y48F, V176E, A204V MUTANT.

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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: 2.45 Å3/Da / Density % sol: 49.82 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 5.5
Details: PCB pH5.0, PEG 1500, pH 5.5, Microbatch, temperature 277K

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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 5, 2008 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 35683 / Num. obs: 34934 / % possible obs: 97.9 % / Redundancy: 5.1 % / Biso Wilson estimate: 19.24 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.051 / Net I/σ(I): 19.6
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.07 / Num. unique all: 3420 / Rsym value: 0.282 / % possible all: 95.3

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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: 3NPU

3npu


Resolution: 2.02→50 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.889 / SU B: 4.2 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26019 1757 5 %RANDOM
Rwork0.20521 ---
obs0.20806 33171 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.241 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å20 Å2-0.4 Å2
2---0.28 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.02→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3640 0 10 157 3807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223765
X-RAY DIFFRACTIONr_bond_other_d0.0140.0210
X-RAY DIFFRACTIONr_angle_refined_deg1.3381.9695103
X-RAY DIFFRACTIONr_angle_other_deg0.618320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2115495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82224.286147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96815641
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8891522
X-RAY DIFFRACTIONr_chiral_restr0.0930.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022780
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210
X-RAY DIFFRACTIONr_nbd_refined0.2040.21856
X-RAY DIFFRACTIONr_nbd_other0.5050.210
X-RAY DIFFRACTIONr_nbtor_refined0.2930.22612
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2189
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2390.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0650.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8561.52550
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30423907
X-RAY DIFFRACTIONr_scbond_it2.32631411
X-RAY DIFFRACTIONr_scangle_it3.6484.51192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.017→2.069 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 113 -
Rwork0.246 2394 -
obs--94.78 %

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