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- PDB-8wps: Anabaena McyI R166M with prebound NAD and malate -

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Basic information

Entry
Database: PDB / ID: 8wps
TitleAnabaena McyI R166M with prebound NAD and malate
ComponentsMcyI
KeywordsOXIDOREDUCTASE / hepatotoxin / microcystin / cofactor / Anabaena
Function / homology(2S)-2-hydroxybutanedioic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesAnabaena sp. 90 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWang, X. / Yin, Y. / Duan, Y. / Liu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2025
Title: Structural insights into the catalytic mechanism of the microcystin tailoring enzyme McyI.
Authors: Wang, X. / Yin, Y. / Cheng, W.L. / Duan, Y.F. / Li, Y.S. / Wang, J. / Wang, M. / Dai, H.E. / Liu, L.
History
DepositionOct 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7333
Polymers38,9361
Non-polymers7982
Water4,576254
1
A: McyI
hetero molecules

A: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4676
Polymers77,8722
Non-polymers1,5954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7560 Å2
ΔGint-31 kcal/mol
Surface area25060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.081, 61.081, 173.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

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Components

#1: Protein McyI


Mass: 38935.949 Da / Num. of mol.: 1 / Mutation: R166M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. 90 (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.01 M tri-Sodium citrate , 16% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30403 / % possible obs: 100 % / Redundancy: 11 % / CC1/2: 0.994 / CC star: 0.998 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.036 / Rrim(I) all: 0.121 / Χ2: 1.091 / Net I/σ(I): 5.5 / Num. measured all: 335464
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.9-1.9711.31.26629920.7060.910.3891.3250.967100
1.97-2.0510.70.82929590.8470.9580.2620.870.962100
2.05-2.1411.30.57529640.9290.9810.1760.6021.017100
2.14-2.2511.60.41930190.9590.9890.1270.4381.09499.9
2.25-2.3911.20.30429840.9770.9940.0940.3191.093100
2.39-2.5810.80.20230250.9870.9970.0630.2121.127100
2.58-2.8411.50.15530120.9920.9980.0470.1621.171100
2.84-3.2510.80.11430650.9940.9990.0360.1191.19299.9
3.25-4.0911.30.08731020.9960.9990.0270.0911.152100
4.09-509.90.07432810.9960.9990.0240.0781.12899.9

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WWK

1wwk


Resolution: 1.9→30.54 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 1513 4.99 %
Rwork0.1709 --
obs0.1727 30329 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→30.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2489 0 9 254 2752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072576
X-RAY DIFFRACTIONf_angle_d0.9933516
X-RAY DIFFRACTIONf_dihedral_angle_d15.557953
X-RAY DIFFRACTIONf_chiral_restr0.066421
X-RAY DIFFRACTIONf_plane_restr0.006446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.24811020.25072562X-RAY DIFFRACTION99
1.96-2.030.26291380.20962592X-RAY DIFFRACTION100
2.03-2.110.23151600.20092547X-RAY DIFFRACTION100
2.11-2.210.24671510.19172566X-RAY DIFFRACTION100
2.21-2.330.25081340.18852568X-RAY DIFFRACTION100
2.33-2.470.221390.17942604X-RAY DIFFRACTION100
2.47-2.660.23441390.18042623X-RAY DIFFRACTION100
2.66-2.930.20521680.18812587X-RAY DIFFRACTION100
2.93-3.350.23471050.17652661X-RAY DIFFRACTION100
3.35-4.220.20861220.15872709X-RAY DIFFRACTION100
4.22-30.540.16381550.1482797X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -14.6814 Å / Origin y: 8.1998 Å / Origin z: -4.5189 Å
111213212223313233
T0.3167 Å20.0024 Å20.0138 Å2-0.2372 Å2-0.0431 Å2--0.286 Å2
L0.4495 °2-0.2985 °2-0.11 °2-0.4495 °2-0.469 °2--0.5347 °2
S0.0777 Å °-0.0563 Å °0.0649 Å °-0.0753 Å °-0.0162 Å °0.0009 Å °-0.0888 Å °-0.0649 Å °0 Å °
Refinement TLS groupSelection details: all

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