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- PDB-8qcj: Crystal structure of mycothiol disulfide reductase Mtr from Rhodo... -

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Basic information

Entry
Database: PDB / ID: 8qcj
TitleCrystal structure of mycothiol disulfide reductase Mtr from Rhodococcus erythropolis
ComponentsMycothione reductase
KeywordsOXIDOREDUCTASE / DISULFIDE REDUCTASE / FAD / FLAVOPROTEIN / MYCOTHIONE REDUCTASE
Function / homology
Function and homology information


mycothione reductase / mycothione reductase [NAD(P)H] activity / nucleotide binding
Similarity search - Function
Mycothione reductase / Pyridine nucleotide-disulphide oxidoreductase, class I / Pyridine nucleotide-disulphide oxidoreductase, class I, active site / Pyridine nucleotide-disulphide oxidoreductases class-I active site. / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / Pyridine nucleotide-disulphide oxidoreductase, dimerisation domain / FAD/NAD-linked reductase, dimerisation domain superfamily / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Mycothione reductase
Similarity search - Component
Biological speciesRhodococcus erythropolis PR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsGutierrez-Fernandez, J. / Hammerstad, M. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Research Council of Norway144971 Norway
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: The crystal structure of mycothiol disulfide reductase (Mtr) provides mechanistic insight into the specific low-molecular-weight thiol reductase activity of Actinobacteria.
Authors: Gutierrez-Fernandez, J. / Hersleth, H.P. / Hammerstad, M.
History
DepositionAug 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mycothione reductase
B: Mycothione reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,3224
Polymers98,7512
Non-polymers1,5712
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9880 Å2
ΔGint-52 kcal/mol
Surface area34240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.965, 92.965, 100.223
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Mycothione reductase


Mass: 49375.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus erythropolis PR4 (bacteria)
Gene: mtr, RER_26020 / Production host: Escherichia coli (E. coli) / References: UniProt: C0ZY75, mycothione reductase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
Has ligand of interestY
Has protein modificationY

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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: 2.53 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 45% (w/v) polypropylene glycol 400 and 4% (v/v) ethanol, and protein concentration of 30 mg/mL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87311 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87311 Å / Relative weight: 1
ReflectionResolution: 2.9→46.48 Å / Num. obs: 21492 / % possible obs: 100 % / Redundancy: 10.2 % / CC1/2: 0.997 / Rmerge(I) obs: 0.209 / Rpim(I) all: 0.069 / Rrim(I) all: 0.22 / Net I/σ(I): 10.1
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.724 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3468 / CC1/2: 0.593 / Rpim(I) all: 0.561 / Rrim(I) all: 1.814 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→46.48 Å / Cross valid method: FREE R-VALUE / σ(F): 281.02 / Phase error: 24.11 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2234 1031 4.8 %
Rwork0.1766 --
obs0.1797 21470 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refine analyzeLuzzati coordinate error obs: 0.505 Å
Refinement stepCycle: LAST / Resolution: 2.9→46.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6944 0 106 0 7050
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037184
X-RAY DIFFRACTIONf_angle_d0.7529780
X-RAY DIFFRACTIONf_dihedral_angle_d8.699998
X-RAY DIFFRACTIONf_chiral_restr0.0471116
X-RAY DIFFRACTIONf_plane_restr0.0071268
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.050.2981480.2782917X-RAY DIFFRACTION95
3.05-3.240.30571220.26552957X-RAY DIFFRACTION96
3.24-3.490.27771860.22682877X-RAY DIFFRACTION94
3.5-3.850.25171600.19622919X-RAY DIFFRACTION95
3.85-4.40.1931730.16312880X-RAY DIFFRACTION94
4.4-5.540.16851280.13682943X-RAY DIFFRACTION96
5.55-46.480.21281140.1492946X-RAY DIFFRACTION96
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)
10.8345-0.1348-0.57492.8494-1.11952.0419-0.3703-0.2319-0.14020.40760.3304-0.25970.42210.33520.1091.06220.1061-0.14710.68010.02120.5337-10.986338.036112.9877
23.7970.8762-0.76182.6890.15343.6166-0.08510.10270.1956-0.0864-0.1133-0.29940.44340.5666-0.01540.70040.055-0.0160.31620.04530.5553-8.461548.4203-9.4895
30.75820.8227-0.2692.6025-2.20342.3349-0.2503-0.07-0.2309-0.67860.1166-0.32911.18050.04510.20391.33570.2573-0.00640.6275-0.06110.5765-12.406627.690.5462
41.6986-0.4658-0.540.9020.08590.44850.10050.68310.0402-0.1059-0.17280.26440.9564-0.5072-0.01721.2829-0.2915-0.16170.5313-0.06170.4198-35.292939.4028-5.386
51.68231.04570.69931.65160.18551.28530.32850.08880.422-1.2046-0.3894-0.29110.0858-0.8653-0.24690.6273-0.1328-0.03541.19650.04180.9163-63.977858.1621-10.082
62.494-0.698-0.87732.6277-0.69672.542-0.12030.23610.7944-0.07350.0655-0.38110.3439-0.27260.29580.3512-0.00590.05920.30040.02010.6642-37.386567.5589-1.4098
72.58920.44081.05622.9425-0.15470.5343-0.13190.11860.2496-0.2677-0.18290.3360.0727-1.0389-0.08170.5318-0.1515-0.00521.21140.10450.5573-66.047766.8221-1.4346
82.1457-0.2969-0.29461.3727-0.09061.34560.1758-0.1173-0.05460.1885-0.3759-0.0337-0.0094-0.1775-0.0170.50260.0249-0.0880.51160.07170.4426-43.732269.192514.1837
95.0638-2.7045-0.41864.58110.35881.31320.0581-0.17820.58160.5074-0.0314-0.97240.1509-0.21420.25410.6663-0.0012-0.01710.59030.05480.4299-44.052770.460622.4871
101.1861-0.1942-0.0912.59641.13250.7587-0.04180.2454-0.16610.5401-0.26660.22050.4367-1.05230.07190.7281-0.52270.03010.9816-0.05160.4994-62.757856.83876.1943
112.8374-0.1356-0.60051.61520.31651.43910.2384-0.02660.26390.2882-0.22320.15940.7064-0.53480.03240.7639-0.1568-0.05630.52990.03570.3498-43.763444.88112.5168
122.7796-0.15220.38791.461.01121.594-0.39210.0418-0.2831-0.03680.2255-0.64131.34120.245-0.04831.0089-0.1205-0.02490.42020.07060.4071-33.100336.3910.8038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 245 )
3X-RAY DIFFRACTION3chain 'A' and (resid 246 through 325 )
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 458 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 43 )
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 100 )
7X-RAY DIFFRACTION7chain 'B' and (resid 101 through 160 )
8X-RAY DIFFRACTION8chain 'B' and (resid 161 through 208 )
9X-RAY DIFFRACTION9chain 'B' and (resid 209 through 245 )
10X-RAY DIFFRACTION10chain 'B' and (resid 246 through 325 )
11X-RAY DIFFRACTION11chain 'B' and (resid 326 through 426 )
12X-RAY DIFFRACTION12chain 'B' and (resid 427 through 458 )

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