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- PDB-5d33: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 12... -

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Basic information

Entry
Database: PDB / ID: 5d33
TitleDirected evolutionary changes in Kemp Eliminase KE07 - Crystal 12 round 7
Componentsde novo kemp eliminase KE07 round 7
KeywordsDE NOVO PROTEIN / LYASE / Kemp Eliminase / Directed Evolution / KE07
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsJackson, C.J. / Hong, N.-S. / Carr, P.D.
CitationJournal: To Be Published
Title: Directed evolutionary changes in Kemp Eliminase KE07 - Crystal 12 round 7
Authors: Hong, N.-S. / Jackson, C.J. / Carr, P.D.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: de novo kemp eliminase KE07 round 7
B: de novo kemp eliminase KE07 round 7


Theoretical massNumber of molelcules
Total (without water)57,9622
Polymers57,9622
Non-polymers00
Water7,710428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.984, 82.722, 176.972
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein de novo kemp eliminase KE07 round 7


Mass: 28980.986 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 11% (W/V) PEG 3350, 0.1M BIS-TRIS PROPANE, PH 8.5, 0.2M NAF

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.59→44.24 Å / Num. obs: 76765 / % possible obs: 98.22 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.1134 / Net I/σ(I): 13.54

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IIV

3iiv


Resolution: 1.59→38.071 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 3853 5.02 %
Rwork0.1991 --
obs0.2006 76760 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.59→38.071 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3997 0 0 428 4425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074164
X-RAY DIFFRACTIONf_angle_d1.0345633
X-RAY DIFFRACTIONf_dihedral_angle_d12.861547
X-RAY DIFFRACTIONf_chiral_restr0.042642
X-RAY DIFFRACTIONf_plane_restr0.005729
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.60940.25171400.22292542X-RAY DIFFRACTION97
1.6094-1.62980.23221500.21422554X-RAY DIFFRACTION97
1.6298-1.65120.24331110.2082514X-RAY DIFFRACTION97
1.6512-1.67380.25741320.20422528X-RAY DIFFRACTION97
1.6738-1.69780.2551320.20562611X-RAY DIFFRACTION97
1.6978-1.72310.2441300.19842505X-RAY DIFFRACTION97
1.7231-1.750.23421270.20452558X-RAY DIFFRACTION98
1.75-1.77870.21521300.21562596X-RAY DIFFRACTION98
1.7787-1.80940.2721230.22422541X-RAY DIFFRACTION98
1.8094-1.84230.26821420.22042561X-RAY DIFFRACTION98
1.8423-1.87770.25771370.22152575X-RAY DIFFRACTION98
1.8777-1.9160.27111260.22322565X-RAY DIFFRACTION98
1.916-1.95770.2531340.23782613X-RAY DIFFRACTION98
1.9577-2.00320.29041430.23412542X-RAY DIFFRACTION98
2.0032-2.05330.25181270.2252640X-RAY DIFFRACTION98
2.0533-2.10890.27021310.22192553X-RAY DIFFRACTION98
2.1089-2.17090.24641600.22152627X-RAY DIFFRACTION99
2.1709-2.2410.21841330.22062566X-RAY DIFFRACTION99
2.241-2.3210.24221490.21222611X-RAY DIFFRACTION99
2.321-2.4140.23681490.21842614X-RAY DIFFRACTION99
2.414-2.52380.27171340.21612618X-RAY DIFFRACTION98
2.5238-2.65680.26171500.21382625X-RAY DIFFRACTION99
2.6568-2.82320.2431440.21682648X-RAY DIFFRACTION99
2.8232-3.04110.25571330.20692657X-RAY DIFFRACTION99
3.0411-3.3470.22741420.18912662X-RAY DIFFRACTION99
3.347-3.8310.19891630.17012688X-RAY DIFFRACTION99
3.831-4.82510.16631310.14942729X-RAY DIFFRACTION99
4.8251-38.08210.17941500.17582864X-RAY DIFFRACTION99

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