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- PDB-5ng7: Novel epoxide hydrolases belonging to the alpha/beta hydrolases s... -

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Basic information

Entry
Database: PDB / ID: 5ng7
TitleNovel epoxide hydrolases belonging to the alpha/beta hydrolases superfamily in metagenomes from hot environments
Componentsepoxide hydrolase
KeywordsHYDROLASE / Epoxide hydrolases / metagenomics / industrial biocatalysis / stereoselectivity / protein structure
Function / homologyAlpha/Beta hydrolase fold, catalytic domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / SERINE
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsFerrandi, E.E. / De Rose, S.A. / Sayer, C. / Guazzelli, E. / Marchesi, C. / Saneei, V. / Isupov, M.N. / Littlechild, J.A. / Monti, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European UnionFP7/2007-2013 HOTZYME United Kingdom
CitationJournal: Front Bioeng Biotechnol / Year: 2018
Title: New Thermophilic alpha / beta Class Epoxide Hydrolases Found in Metagenomes From Hot Environments.
Authors: Ferrandi, E.E. / Sayer, C. / De Rose, S.A. / Guazzelli, E. / Marchesi, C. / Saneei, V. / Isupov, M.N. / Littlechild, J.A. / Monti, D.
History
DepositionMar 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._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 / _citation_author.name
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: epoxide hydrolase
B: epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,38510
Polymers69,8812
Non-polymers5048
Water11,097616
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-33 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.940, 46.220, 73.870
Angle α, β, γ (deg.)90.00, 106.94, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 2 - 290 / Label seq-ID: 2 - 290

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein epoxide hydrolase


Mass: 34940.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli) / References: soluble epoxide hydrolase

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Non-polymers , 5 types, 624 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 1.92 Å3/Da / Density % sol: 35.79 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 7.5
Details: 200 mM Magnesium formate dehydrate, 100mM Sodium Hepes 7.5 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→39.51 Å / Num. obs: 104819 / % possible obs: 98.2 % / Redundancy: 3.2 % / Biso Wilson estimate: 24.9 Å2 / Rsym value: 0.035 / Net I/σ(I): 15.6
Reflection shellResolution: 1.39→1.41 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4187 / CC1/2: 0.483 / Rsym value: 0.77 / % possible all: 79

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4inz

4inz


Resolution: 1.39→39.51 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.965 / SU B: 1.473 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.20373 5200 5 %RANDOM
Rwork0.17257 ---
obs0.17413 99619 98.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.809 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å2-0.18 Å2
2--0.61 Å20 Å2
3---0.14 Å2
Refinement stepCycle: 1 / Resolution: 1.39→39.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 29 616 5437
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195664
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9647809
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7725758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.45824.079277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15151095
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7421533
X-RAY DIFFRACTIONr_chiral_restr0.1140.2856
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0214351
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.7165.5332554
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.2749.2863239
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.0556.583110
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined8.23241.36324805
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 21536 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 323 -
Rwork0.315 6061 -
obs--81.44 %

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