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- PDB-4o5s: Crystal structure of Diels-Alderase CE11 -

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Basic information

Entry
Database: PDB / ID: 4o5s
TitleCrystal structure of Diels-Alderase CE11
ComponentsDiisopropyl-fluorophosphatase
KeywordsDe Novo Protein / Hydrolase / protein engineering / computer-aided design / Diels-Alder reaction / enzyme design / directed evolution / substrate specificity / beta-propeller / helix-loop-helix / artificial catalyst / Diels-Alderase / catalyst for cycloaddition
Function / homology
Function and homology information


diisopropyl-fluorophosphatase / diisopropyl-fluorophosphatase activity / calcium ion binding
Similarity search - Function
: / SMP-30/Gluconolactonase/LRE-like region / SMP-30/Gluconolactonase/LRE-like region / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
Diisopropyl-fluorophosphatase
Similarity search - Component
Biological speciesLoligo vulgaris (squid)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBeck, T. / Preiswerk, N. / Mayer, C. / Hilvert, D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase.
Authors: Preiswerk, N. / Beck, T. / Schulz, J.D. / Milovnik, P. / Mayer, C. / Siegel, J.B. / Baker, D. / Hilvert, D.
History
DepositionDec 20, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Aug 24, 2022Group: Database references / Category: citation / database_2 / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Diisopropyl-fluorophosphatase
B: Diisopropyl-fluorophosphatase


Theoretical massNumber of molelcules
Total (without water)74,5162
Polymers74,5162
Non-polymers00
Water2,432135
1
A: Diisopropyl-fluorophosphatase


Theoretical massNumber of molelcules
Total (without water)37,2581
Polymers37,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Diisopropyl-fluorophosphatase


Theoretical massNumber of molelcules
Total (without water)37,2581
Polymers37,2581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.04, 46.15, 76.91
Angle α, β, γ (deg.)84.12, 83.01, 66.18
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Diisopropyl-fluorophosphatase / Diels-Alderase C11 / DFPase


Mass: 37258.211 Da / Num. of mol.: 2
Mutation: V13M, A21T, I33V, 36-PYVEVNGKPA-45 replaced by 36-SPLSEALTKANSPAEAYKASRGA-58, R63H, I85S, A87I, D113E, R128C, E151G, Q162R, A186C, K223N, D245V, S284A, A285N, E301D, L322S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Loligo vulgaris (squid) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIG4, EC: 3.1.8.2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 36-PEVEVNGKPA-45 IN UNP HAS BEEN REPLACED BY 36-SPLSEALTKANSPAEAYKASRGA-58.

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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: 1.86 Å3/Da / Density % sol: 33.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: protein solution (11.7 mg/mL, in 25 mM HEPES, pH 7.5, 150 mM NaCl) was mixed with reservoir solution containing 24.0% w/v PEG 3350 and 0.2 M ammonium nitrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 2, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→42.2 Å / Num. obs: 47771 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.0488 / Net I/σ(I): 14
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.48 % / Rmerge(I) obs: 0.237 / Mean I/σ(I) obs: 3.94 / Num. unique all: 6849 / % possible all: 92.3

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
XDSdata reduction
SADABSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E1A

1e1a


Resolution: 1.8→42.15 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.039 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23266 2389 5 %RANDOM
Rwork0.18485 ---
obs0.1872 45382 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.032 Å2
Baniso -1Baniso -2Baniso -3
1--1.53 Å2-0.73 Å2-0.32 Å2
2--1.35 Å21.13 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 1.8→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4713 0 0 135 4848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194849
X-RAY DIFFRACTIONr_bond_other_d0.0010.024415
X-RAY DIFFRACTIONr_angle_refined_deg1.711.946603
X-RAY DIFFRACTIONr_angle_other_deg0.832310152
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3115636
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.78724.845194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.13715716
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8951512
X-RAY DIFFRACTIONr_chiral_restr0.1030.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215632
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021104
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_it2.3832.8782541
X-RAY DIFFRACTIONr_mcbond_other2.3822.8762540
X-RAY DIFFRACTIONr_mcangle_it3.3154.3043172
X-RAY DIFFRACTIONr_mcangle_other3.3154.3063173
X-RAY DIFFRACTIONr_scbond_it2.6453.0642308
X-RAY DIFFRACTIONr_scbond_other2.6443.0652309
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.854.4973429
X-RAY DIFFRACTIONr_long_range_B_refined5.30123.3395226
X-RAY DIFFRACTIONr_long_range_B_other5.28423.3065187
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 164 -
Rwork0.224 3111 -
obs--88.51 %

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