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- PDB-8d4w: Asymmetric ene-reduction of alpha,beta-unsaturated compounds usin... -

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Basic information

Entry
Database: PDB / ID: 8d4w
TitleAsymmetric ene-reduction of alpha,beta-unsaturated compounds using MSMEG_2850
ComponentsCell entry (Mce) related family protein
KeywordsOXIDOREDUCTASE / F420 / FDOR
Function / homologyF420H(2)-dependent quinone reductase / F420H(2)-dependent quinone reductase / FMN-binding split barrel / Oxidoreductases / oxidoreductase activity / DI(HYDROXYETHYL)ETHER / Cell entry (Mce) related family protein
Function and homology information
Biological speciesMycolicibacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsKang, S.W. / Frkic, R.L. / Jackson, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2023
Title: Asymmetric Ene-Reduction of alpha , beta-Unsaturated Compounds by F 420 -Dependent Oxidoreductases A Enzymes from Mycobacterium smegmatis .
Authors: Kang, S.W. / Antoney, J. / Frkic, R.L. / Lupton, D.W. / Speight, R. / Scott, C. / Jackson, C.J.
History
DepositionJun 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 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: Cell entry (Mce) related family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8455
Polymers15,4621
Non-polymers3824
Water2,378132
1
A: Cell entry (Mce) related family protein
hetero molecules

A: Cell entry (Mce) related family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,69010
Polymers30,9252
Non-polymers7658
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation37_544y+1/4,x-1/4,-z-1/41
Buried area4930 Å2
ΔGint-23 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.809, 128.809, 128.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-397-

HOH

21A-413-

HOH

31A-414-

HOH

41A-415-

HOH

51A-416-

HOH

61A-427-

HOH

71A-431-

HOH

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Components

#1: Protein Cell entry (Mce) related family protein


Mass: 15462.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Gene: ddn_5, NCTC7017_06025 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8B4R830, Oxidoreductases
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.88 Å3/Da / Density % sol: 57.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 1.3 M potassium phosphate, 0.7 M sodium phosphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.35→45.54 Å / Num. obs: 40092 / % possible obs: 100 % / Redundancy: 76.5 % / Biso Wilson estimate: 22.12 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.135 / Net I/σ(I): 23.8 / Num. measured all: 3067306 / Scaling rejects: 2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.35-1.37799.9919530.351100
7.4-45.5459.70.0423060.999199.7

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Y9I

4y9i


Resolution: 1.35→45.54 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2025 1997 4.98 %
Rwork0.1883 38072 -
obs0.1891 40069 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.84 Å2 / Biso mean: 31.1122 Å2 / Biso min: 15.56 Å2
Refinement stepCycle: final / Resolution: 1.35→45.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1061 0 25 132 1218
Biso mean--36.98 38.59 -
Num. residues----136
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.35-1.380.45971410.428326762817
1.38-1.420.35341230.341526872810
1.42-1.460.30171590.28426632822
1.46-1.510.25861480.238926682816
1.51-1.560.21971350.219126872822
1.56-1.630.24921450.205426832828
1.63-1.70.21541250.206927072832
1.7-1.790.23981290.214327102839
1.79-1.90.21991610.18826982859
1.9-2.050.19081190.175227292848
2.05-2.260.19371510.180527152866
2.26-2.580.20351570.185527352892
2.58-3.250.1831520.18627812933
3.25-45.540.18721520.170729333085
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)
17.60862.37774.83016.41051.81839.3288-0.0869-0.41060.65680.3872-0.1163-1.0712-0.33230.9680.05760.2995-0.0423-0.04150.4648-0.02460.484924.7748-1.0787-22.1278
29.9668-6.13724.29039.7563-6.68874.6197-0.1748-0.31390.3160.2168-0.0875-0.1847-0.12890.88340.2040.32020.0479-0.01950.345-0.07010.328322.673-12.0771-21.9227
31.5693-0.1742-0.91791.3777-0.59633.97040.00770.10210.0087-0.03270.04580.0231-0.1411-0.1262-0.05530.15620.03150.01480.15750.00290.13997.0716-5.0755-16.6634
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 21 )A5 - 21
2X-RAY DIFFRACTION2chain 'A' and (resid 22 through 34 )A22 - 34
3X-RAY DIFFRACTION3chain 'A' and (resid 35 through 140 )A35 - 140

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