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- PDB-8acv: WelO5* bound to Zn(II), Cl, and 2-oxoglutarate -

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Basic information

Entry
Database: PDB / ID: 8acv
TitleWelO5* bound to Zn(II), Cl, and 2-oxoglutarate
ComponentsOxidoreductase
KeywordsOXIDOREDUCTASE / WelO5* 2-oxoglutarate-dependent halogenase
Function / homology: / Carrier-protein-independent halogenase WelO5 / metal ion binding / ACETATE ION / 2-OXOGLUTARIC ACID / Oxidoreductase
Function and homology information
Biological speciesHapalosiphon welwitschii UH IC-52-3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsBuller, R. / Hueppi, S. / Voss, M. / Hayashi, T.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Chemcatchem / Year: 2022
Title: Enzyme engineering enables inversion of substrate stereopreference of the halogenase WelO5*
Authors: Voss, M. / Huppi, S. / Schaub, D. / Hayashi, T. / Ligibel, M. / Sager, E. / Schroer, K. / Snajdrova, R. / Buller, R.M.U.
History
DepositionJul 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,44018
Polymers69,2242
Non-polymers1,21716
Water1,09961
1
A: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,37111
Polymers34,6121
Non-polymers75910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0697
Polymers34,6121
Non-polymers4576
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.321, 83.097, 144.318
Angle α, β, γ (deg.)90.00, 96.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-432-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Oxidoreductase


Mass: 34611.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hapalosiphon welwitschii UH IC-52-3 (bacteria)
Gene: welO15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A075X7C6

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Non-polymers , 6 types, 77 molecules

#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.95 Å3/Da / Density % sol: 36.9 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 22.14% PEG-4000, 30 mM sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 2.26→47.77 Å / Num. obs: 25004 / % possible obs: 98.4 % / Redundancy: 5.4 % / Biso Wilson estimate: 58.09 Å2 / CC1/2: 0.999 / Net I/σ(I): 15.1
Reflection shellResolution: 2.269→2.281 Å / Num. unique obs: 2283 / Rrim(I) all: 0.174

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata scaling
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IQS

5iqs


Resolution: 2.26→47.77 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.344 / SU Rfree Blow DPI: 0.222 / SU Rfree Cruickshank DPI: 0.23
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1229 5 %RANDOM
Rwork0.195 ---
obs0.197 24576 98.3 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4154 Å20 Å20.1144 Å2
2---21.0632 Å20 Å2
3---27.4786 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.26→47.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 72 61 4532
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084573HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.036183HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1569SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes789HARMONIC5
X-RAY DIFFRACTIONt_it4573HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.51
X-RAY DIFFRACTIONt_other_torsion19.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion578SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5370SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.28 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.5026 -4.88 %
Rwork0.4279 468 -
all0.4317 492 -
obs--88.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.50330.54841.51381.29370.22797.63690.09320.03550.263-0.0468-0.1024-0.1178-0.26760.0660.0092-0.1703-0.03150.0362-0.319-0.012-0.11139.2706-2.426918.0941
23.44870.4746-0.04391.211-0.48454.6651-0.0756-0.6599-0.163-0.07190.0812-0.01540.3628-0.2847-0.0056-0.1882-0.1035-0.02250.44540.0464-0.36211.1581-17.466454.0418
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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