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- PDB-9jnq: dehydrogenase McyI -

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Basic information

Entry
Database: PDB / ID: 9jnq
Titledehydrogenase McyI
ComponentsMcyI
KeywordsTOXIN / complex / NDA-Mdh
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / amino acid biosynthetic process / NAD binding
Similarity search - Function
: / D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature. / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1 / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain / D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / McyI
Similarity search - Component
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsXue, C. / Wang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32170138 China
CitationJournal: To Be Published
Title: McyI: A Moonlighting Protein Central to Microcystin-LR Biosynthesis and the Fine-Tuned Self-Detoxification Mechanism
Authors: Xue, C. / Wang, Q.
History
DepositionSep 23, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: McyI
B: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7055
Polymers72,2842
Non-polymers1,4223
Water12,683704
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3920 Å2
ΔGint-26 kcal/mol
Surface area30290 Å2
2
B: McyI
hetero molecules

A: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7055
Polymers72,2842
Non-polymers1,4223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area7430 Å2
ΔGint-49 kcal/mol
Surface area26780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.110, 100.983, 131.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein McyI


Mass: 36141.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria)
Gene: mcyI / Production host: Escherichia coli (E. coli) / References: UniProt: J9WTS5
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 704 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.39 Å3/Da / Density % sol: 48.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.05M Tris pH 8.5, 0.1M Li sulfate, 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 28, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.6→13 Å / Num. obs: 91561 / % possible obs: 99.69 % / Redundancy: 13 % / CC1/2: 0.995 / Net I/σ(I): 9.2
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 8533 / CC1/2: 0.85

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.20.1refinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→12.96 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 4534 4.95 %
Rwork0.1987 --
obs0.2005 91561 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→12.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 93 704 5852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d0.957
X-RAY DIFFRACTIONf_dihedral_angle_d16.4451918
X-RAY DIFFRACTIONf_chiral_restr0.058852
X-RAY DIFFRACTIONf_plane_restr0.01899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.27961230.25272823X-RAY DIFFRACTION97
1.62-1.640.2871490.25662857X-RAY DIFFRACTION99
1.64-1.660.27551410.24012853X-RAY DIFFRACTION99
1.66-1.680.26941560.24022866X-RAY DIFFRACTION100
1.68-1.70.271460.23462883X-RAY DIFFRACTION100
1.7-1.720.25831420.22772876X-RAY DIFFRACTION100
1.72-1.750.2531450.22022896X-RAY DIFFRACTION100
1.75-1.770.25581390.21182859X-RAY DIFFRACTION100
1.77-1.80.21931610.21062870X-RAY DIFFRACTION100
1.8-1.830.23351400.21092865X-RAY DIFFRACTION100
1.83-1.860.25721530.21272948X-RAY DIFFRACTION100
1.86-1.90.22391300.22222852X-RAY DIFFRACTION100
1.9-1.930.25251430.24082909X-RAY DIFFRACTION100
1.93-1.970.26321450.21872858X-RAY DIFFRACTION100
1.97-2.010.26351570.21282910X-RAY DIFFRACTION100
2.01-2.060.25121720.21552848X-RAY DIFFRACTION100
2.06-2.110.25911450.2132890X-RAY DIFFRACTION100
2.11-2.170.2111170.18772955X-RAY DIFFRACTION100
2.17-2.230.23831640.19852859X-RAY DIFFRACTION100
2.23-2.30.25561760.21262849X-RAY DIFFRACTION99
2.3-2.390.22511630.1982909X-RAY DIFFRACTION100
2.39-2.480.24481570.20362923X-RAY DIFFRACTION100
2.48-2.590.22311590.20532898X-RAY DIFFRACTION100
2.59-2.730.24021610.20932913X-RAY DIFFRACTION100
2.73-2.90.24031420.2112955X-RAY DIFFRACTION100
2.9-3.120.27251670.20592902X-RAY DIFFRACTION100
3.12-3.430.2191710.19552940X-RAY DIFFRACTION100
3.43-3.910.20471650.16852963X-RAY DIFFRACTION100
3.91-4.880.20641550.15383005X-RAY DIFFRACTION100
4.88-100.21500.17413093X-RAY DIFFRACTION99

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