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- PDB-5od1: Structure of the engineered metalloesterase MID1sc10 complexed wi... -

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Basic information

Entry
Database: PDB / ID: 5od1
TitleStructure of the engineered metalloesterase MID1sc10 complexed with a phosphonate transition state analogue
ComponentsMID1sc10
KeywordsDe Novo Protein/Hydrolase / directed evolution / engineered Metalloenzyme / DE NOVO PROTEIN-HYDROLASE / De Novo Protein-Hydrolase complex
Function / homologyChem-9RQ
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.34 Å
AuthorsMittl, P.R.E. / Studer, S. / Hansen, D.A. / Hilvert, D.
CitationJournal: Science / Year: 2018
Title: Evolution of a highly active and enantiospecific metalloenzyme from short peptides.
Authors: Studer, S. / Hansen, D.A. / Pianowski, Z.L. / Mittl, P.R.E. / Debon, A. / Guffy, S.L. / Der, B.S. / Kuhlman, B. / Hilvert, D.
History
DepositionJul 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2May 29, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MID1sc10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4514
Polymers10,8691
Non-polymers5823
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint0 kcal/mol
Surface area5990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.349, 46.877, 112.621
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein MID1sc10


Mass: 10869.072 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-9RQ / [2-oxidanylidene-7-[oxidanyl-[(1~{S})-1-phenylethyl]phosphoryl]oxy-chromen-4-yl]methanesulfonic acid


Mass: 424.362 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H17O8PS
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 1.96 Å3/Da / Density % sol: 37.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.6
Details: 200 mM HEPES pH 8.6, 14% (w/v) Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.34→43 Å / Num. obs: 19644 / % possible obs: 99.3 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Net I/σ(I): 12.91
Reflection shellResolution: 1.34→1.42 Å / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 1.4 / CC1/2: 0.749 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 1.34→43 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.979 / SU B: 2.619 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.052 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17113 983 5 %RANDOM
Rwork0.12639 ---
obs0.12867 18661 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.207 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å20 Å2-0 Å2
2--0.32 Å2-0 Å2
3---1.5 Å2
Refinement stepCycle: 1 / Resolution: 1.34→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms745 0 35 97 877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.019840
X-RAY DIFFRACTIONr_bond_other_d0.0020.02742
X-RAY DIFFRACTIONr_angle_refined_deg1.7061.9431141
X-RAY DIFFRACTIONr_angle_other_deg1.0512.9721726
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8475103
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.40124.41943
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.26715145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.981157
X-RAY DIFFRACTIONr_chiral_restr0.1260.2117
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02962
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02176
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_it3.3962.265400
X-RAY DIFFRACTIONr_mcbond_other3.3482.247399
X-RAY DIFFRACTIONr_mcangle_it3.9393.387507
X-RAY DIFFRACTIONr_mcangle_other3.943.402508
X-RAY DIFFRACTIONr_scbond_it4.9582.743439
X-RAY DIFFRACTIONr_scbond_other4.9742.739435
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3983.968629
X-RAY DIFFRACTIONr_long_range_B_refined6.56129.5081051
X-RAY DIFFRACTIONr_long_range_B_other6.4728.7681028
X-RAY DIFFRACTIONr_rigid_bond_restr2.93131579
X-RAY DIFFRACTIONr_sphericity_free34.689548
X-RAY DIFFRACTIONr_sphericity_bonded18.54851613
LS refinement shellResolution: 1.34→1.374 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 70 -
Rwork0.329 1323 -
obs--98.38 %

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