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- PDB-6fhf: Highly active enzymes by automated modular backbone assembly and ... -

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Basic information

Entry
Database: PDB / ID: 6fhf
TitleHighly active enzymes by automated modular backbone assembly and sequence design
ComponentsDesign
KeywordsArtificial enzyme / Design
Function / homologyGlycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLapidot, G. / Khersonsky, O. / Lipsh, R. / Dym, O. / Albeck, S. / Rogotner, S. / Fleishman, J.S.
CitationJournal: Nat Commun / Year: 2018
Title: Highly active enzymes by automated combinatorial backbone assembly and sequence design.
Authors: Lapidoth, G. / Khersonsky, O. / Lipsh, R. / Dym, O. / Albeck, S. / Rogotner, S. / Fleishman, S.J.
History
DepositionJan 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Jan 17, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _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: Design
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4673
Polymers42,4211
Non-polymers462
Water1,62190
1
A: Design
hetero molecules

A: Design
hetero molecules

A: Design
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,4029
Polymers127,2643
Non-polymers1386
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_675-y+1,x-y+2,z1
crystal symmetry operation3_465-x+y-1,-x+1,z1
Buried area5470 Å2
ΔGint-40 kcal/mol
Surface area39490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.969, 128.969, 51.710
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-401-

NA

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Components

#1: Protein Design


Mass: 42421.492 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 1.95 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: (NH4)2H2PO4 0.05M 0.05M Sodium acetate pH=4.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.541 Å
DetectorType: RIGAKU / Detector: AREA DETECTOR / Date: Oct 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.85→46.92 Å / Num. obs: 27384 / % possible obs: 100 % / Observed criterion σ(F): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 24.6 Å2 / Rsym value: 0.073 / Net I/σ(I): 12.7
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 5 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4010 / Rsym value: 0.528 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1692: ???)refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3MMD

3mmd


Resolution: 1.85→37.942 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 23.58
RfactorNum. reflection% reflection
Rfree0.2263 1362 4.97 %
Rwork0.1836 --
obs0.1858 27384 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.85→37.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2928 0 2 90 3020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093018
X-RAY DIFFRACTIONf_angle_d0.9784102
X-RAY DIFFRACTIONf_dihedral_angle_d5.6762528
X-RAY DIFFRACTIONf_chiral_restr0.053423
X-RAY DIFFRACTIONf_plane_restr0.008546
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.91610.32051230.26992632X-RAY DIFFRACTION100
1.9161-1.99280.29361500.22172570X-RAY DIFFRACTION100
1.9928-2.08350.23361140.19632618X-RAY DIFFRACTION100
2.0835-2.19340.25861570.18992592X-RAY DIFFRACTION100
2.1934-2.33080.24241240.19282601X-RAY DIFFRACTION100
2.3308-2.51070.25261480.19382590X-RAY DIFFRACTION100
2.5107-2.76330.24391220.20392620X-RAY DIFFRACTION100
2.7633-3.1630.21141200.19052636X-RAY DIFFRACTION100
3.163-3.98430.20941540.17242566X-RAY DIFFRACTION100
3.9843-37.95030.19441500.1522597X-RAY DIFFRACTION100

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