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- PDB-3nq8: Optimization of the in silico designed Kemp eliminase KE70 by com... -

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Basic information

Entry
Database: PDB / ID: 3nq8
TitleOptimization of the in silico designed Kemp eliminase KE70 by computational design and directed evolution R4 8/5A
Componentsdeoxyribose phosphate aldolase
KeywordsLYASE / TIM / Structural Genomics / Israel Structural Proteomics Center / ISPC
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / BENZAMIDINE / NITRATE ION
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 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 / pdbx_struct_special_symmetry / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7424
Polymers28,4971
Non-polymers2443
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.756, 52.756, 153.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-273-

HOH

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Components

#1: Protein deoxyribose phosphate aldolase


Mass: 28497.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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 0, SER 19, GLY 239 INSERTION AND K28N, Y47F, W71C, H165Y, K196N, A203V 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: 1.88 Å3/Da / Density % sol: 34.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.1M Ammonium Nitrat, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorDetector: CCD / Date: Dec 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 43950 / Num. obs: 43027 / % possible obs: 97.9 % / Redundancy: 20.5 % / Biso Wilson estimate: 14.63 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.053 / Net I/σ(I): 57.28
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 23.1 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 13.6 / Num. unique all: 2163 / Rsym value: 0.211 / % possible all: 100

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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: 1JCJ

1jcj


Resolution: 1.4→49.88 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.549 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 2155 5 %RANDOM
Rwork0.17408 ---
obs0.17492 40785 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.627 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.4→49.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1801 0 17 166 1984
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221846
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.972508
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9285246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.17424.42970
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.88315289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8691510
X-RAY DIFFRACTIONr_chiral_restr0.0710.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211383
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_it0.8241.51230
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35421948
X-RAY DIFFRACTIONr_scbond_it2.1233616
X-RAY DIFFRACTIONr_scangle_it3.1764.5559
X-RAY DIFFRACTIONr_rigid_bond_restr1.24431846
X-RAY DIFFRACTIONr_sphericity_free3.9463166
X-RAY DIFFRACTIONr_sphericity_bonded2.38431821
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.185 150 -
Rwork0.147 3041 -
obs--100 %

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