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- PDB-6unw: Epoxide hydrolase from an endophytic Streptomyces -

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Basic information

Entry
Database: PDB / ID: 6unw
TitleEpoxide hydrolase from an endophytic Streptomyces
ComponentsSoluble epoxide hydrolase
KeywordsHYDROLASE / epoxide hydrolase / biocatalysis
Function / homologyCACODYLATE ION
Function and homology information
Biological speciesStreptomyces sp. CBMAI 2042 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsWilson, C. / dos Santos, J.C. / Dias, M.V.B.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: An epoxide hydrolase from endophytic Streptomyces shows unique structural features and wide biocatalytic activity.
Authors: Tormet-Gonzalez, G.D. / Wilson, C. / de Oliveira, G.S. / Dos Santos, J.C. / de Oliveira, L.G. / Dias, M.V.B.
History
DepositionOct 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)115,32811
Polymers114,7393
Non-polymers5888
Water10,683593
1
A: Soluble epoxide hydrolase
B: Soluble epoxide hydrolase
C: Soluble epoxide hydrolase
hetero molecules

A: Soluble epoxide hydrolase
B: Soluble epoxide hydrolase
C: Soluble epoxide hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,65522
Polymers229,4796
Non-polymers1,17616
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-x,y,-z1
Unit cell
Length a, b, c (Å)106.733, 106.733, 233.039
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

21A-668-

HOH

31C-617-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 through 255 or resid 257 through 334 or resid 401))
21(chain B and (resid 16 through 255 or resid 257 through 334 or resid 401))
31(chain C and (resid 16 through 255 or resid 257 through 334 or resid 401))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASP(chain A and (resid 16 through 255 or resid 257 through 334 or resid 401))AA16 - 25516 - 255
12ASPASPARGARG(chain A and (resid 16 through 255 or resid 257 through 334 or resid 401))AA257 - 334257 - 334
13CACCACCACCAC(chain A and (resid 16 through 255 or resid 257 through 334 or resid 401))AD401
21GLYGLYASPASP(chain B and (resid 16 through 255 or resid 257 through 334 or resid 401))BB16 - 25516 - 255
22ASPASPARGARG(chain B and (resid 16 through 255 or resid 257 through 334 or resid 401))BB257 - 334257 - 334
23CACCACCACCAC(chain B and (resid 16 through 255 or resid 257 through 334 or resid 401))BH401
31GLYGLYASPASP(chain C and (resid 16 through 255 or resid 257 through 334 or resid 401))CC16 - 25516 - 255
32ASPASPARGARG(chain C and (resid 16 through 255 or resid 257 through 334 or resid 401))CC257 - 334257 - 334
33CACCACCACCAC(chain C and (resid 16 through 255 or resid 257 through 334 or resid 401))CJ401

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Components

#1: Protein Soluble epoxide hydrolase


Mass: 38246.430 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CBMAI 2042 (bacteria) / Gene: STAN_0072
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C2H6AsO2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: Tris-citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.21→48.52 Å / Num. obs: 67798 / % possible obs: 99.5 % / Redundancy: 17.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.03 / Rrim(I) all: 0.124 / Net I/σ(I): 21.2 / Num. measured all: 1184544 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.21-2.2611.91.2425085642800.7060.3651.2972.195
10.37-48.5214.20.035111547860.9990.0090.03754.398.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX18.1-3865refinement
XDSdata reduction
Aimless0.2.8data scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E3J

2e3j


Resolution: 2.21→48.52 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2272 3267 5.06 %
Rwork0.1867 61290 -
obs0.1887 64557 94.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.22 Å2 / Biso mean: 39.8035 Å2 / Biso min: 18.66 Å2
Refinement stepCycle: final / Resolution: 2.21→48.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 20 593 8090
Biso mean--61.43 41.57 -
Num. residues----973
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2904X-RAY DIFFRACTION8.693TORSIONAL
12B2904X-RAY DIFFRACTION8.693TORSIONAL
13C2904X-RAY DIFFRACTION8.693TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.21-2.240.34011480.27962520266893
2.24-2.280.32591640.268527632927100
2.28-2.320.46031210.44252066218775
2.32-2.360.7722590.64141026108538
2.36-2.40.4511100.38082103221377
2.4-2.450.24671410.2327772918100
2.45-2.50.31791420.210627662908100
2.5-2.550.26811360.207927892925100
2.55-2.610.29191360.207727882924100
2.61-2.680.23181640.202427652929100
2.68-2.750.26361590.198127852944100
2.75-2.830.23131450.205327792924100
2.83-2.920.23751510.194727622913100
2.92-3.020.23611650.192328002965100
3.02-3.150.22311440.183228182962100
3.15-3.290.17311470.170727922939100
3.29-3.460.19761470.163728082955100
3.46-3.680.20761370.152628332970100
3.68-3.960.17071450.145928542999100
3.96-4.360.16721500.141728222972100
4.36-4.990.17351450.14128883033100
4.99-6.280.21111580.170829343092100
6.29-48.520.19891530.17543052320599
Refinement TLS params.Method: refined / Origin x: 20.9343 Å / Origin y: 31.1737 Å / Origin z: 4.9466 Å
111213212223313233
T0.1927 Å20.016 Å20.013 Å2-0.2323 Å20.0381 Å2--0.2475 Å2
L0.416 °2-0.0179 °20.0178 °2-0.8666 °20.0295 °2--0.3909 °2
S0.0279 Å °0.0486 Å °-0.0738 Å °-0.0478 Å °-0.0474 Å °-0.188 Å °0.0539 Å °0.0847 Å °0.0213 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA14 - 348
2X-RAY DIFFRACTION1allA401
3X-RAY DIFFRACTION1allB14 - 335
4X-RAY DIFFRACTION1allB401
5X-RAY DIFFRACTION1allC16 - 335
6X-RAY DIFFRACTION1allC401
7X-RAY DIFFRACTION1allS1 - 636
8X-RAY DIFFRACTION1allD1 - 5

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