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- PDB-6wup: Crystal structure of an ancestral cyclohexadienyl dehydratase, An... -

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Basic information

Entry
Database: PDB / ID: 6wup
TitleCrystal structure of an ancestral cyclohexadienyl dehydratase, AncCDT-5
ComponentsAncestral cyclohexadienyl dehydratase, AncCDT-5
KeywordsLYASE / cyclohexadienyl dehydratase ancestral protein reconstruction
Function / homologyPeriplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsKaczmarski, J.A. / Mahawaththa, M.C.
Citation
Journal: Nat Commun / Year: 2020
Title: Altered conformational sampling along an evolutionary trajectory changes the catalytic activity of an enzyme.
Authors: Kaczmarski, J.A. / Mahawaththa, M.C. / Feintuch, A. / Clifton, B.E. / Adams, L.A. / Goldfarb, D. / Otting, G. / Jackson, C.J.
#1: Journal: Nat. Chem. Biol. / Year: 2018
Title: Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.
Authors: Clifton, B. / Kaczmarski, J.A. / Carr, P.D. / Gerth, M.L. / Tokuriki, N. / Jackson, C.J.
History
DepositionMay 5, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionMay 13, 2020ID: 6OKI
Revision 1.0May 13, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ancestral cyclohexadienyl dehydratase, AncCDT-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2403
Polymers26,9671
Non-polymers2742
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomeric in solution
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.955, 70.955, 175.390
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-490-

HOH

21A-684-

HOH

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Components

#1: Protein Ancestral cyclohexadienyl dehydratase, AncCDT-5


Mass: 26966.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 % w/v PEG 6000, 0.2 M MgCl2, 0.1 M HEPES, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 1.49→43.85 Å / Num. obs: 43661 / % possible obs: 100 % / Redundancy: 35.3 % / Biso Wilson estimate: 25.82 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.019 / Net I/σ(I): 22.4
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 30.3 % / Rmerge(I) obs: 3.9 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 2105 / CC1/2: 0.501 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OKI

6oki
PDB Unreleased entry


Resolution: 1.49→35.69 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4522
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2217 2209 5.07 %
Rwork0.1975 41351 -
obs0.1987 43560 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.51 Å2
Refinement stepCycle: LAST / Resolution: 1.49→35.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1866 0 16 296 2178
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071944
X-RAY DIFFRACTIONf_angle_d0.89742638
X-RAY DIFFRACTIONf_chiral_restr0.0739280
X-RAY DIFFRACTIONf_plane_restr0.0058347
X-RAY DIFFRACTIONf_dihedral_angle_d15.5091733
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.49-1.520.33461180.30392533X-RAY DIFFRACTION100
1.52-1.560.28961500.2832504X-RAY DIFFRACTION99.96
1.56-1.60.29021510.2652515X-RAY DIFFRACTION100
1.6-1.640.31361280.25142544X-RAY DIFFRACTION100
1.64-1.690.26371380.23252556X-RAY DIFFRACTION100
1.69-1.740.26141360.22672517X-RAY DIFFRACTION99.96
1.74-1.80.25451490.21822552X-RAY DIFFRACTION100
1.81-1.880.23241290.2112553X-RAY DIFFRACTION100
1.88-1.960.25781190.21462576X-RAY DIFFRACTION100
1.96-2.070.23321490.20752538X-RAY DIFFRACTION100
2.07-2.20.23521370.20332600X-RAY DIFFRACTION100
2.2-2.370.25371480.21082584X-RAY DIFFRACTION100
2.37-2.60.23571290.20592606X-RAY DIFFRACTION100
2.6-2.980.24541420.21712635X-RAY DIFFRACTION99.93
2.98-3.750.20241350.18122679X-RAY DIFFRACTION99.96
3.75-35.690.18281510.17112859X-RAY DIFFRACTION99.73

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