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- PDB-8wph: Anabaena McyI with prebound NAD -

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Basic information

Entry
Database: PDB / ID: 8wph
TitleAnabaena McyI with prebound NAD
ComponentsMcyI-NAD
KeywordsOXIDOREDUCTASE / hepatotoxin / microcystin / cofactor / Anabaena
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesAnabaena sp. 90 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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-NAD
B: McyI-NAD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,2514
Polymers77,9242
Non-polymers1,3272
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-41 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.038, 74.038, 128.469
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 17 through 147 or (resid 148...
21(chain B and (resid 17 through 232 or (resid 233...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISASNASN(chain A and (resid 17 through 147 or (resid 148...AA17 - 14737 - 167
12GLNGLNGLNGLN(chain A and (resid 17 through 147 or (resid 148...AA148168
13HISHISNADNAD(chain A and (resid 17 through 147 or (resid 148...AA - C17 - 50137
14HISHISNADNAD(chain A and (resid 17 through 147 or (resid 148...AA - C17 - 50137
15HISHISNADNAD(chain A and (resid 17 through 147 or (resid 148...AA - C17 - 50137
16HISHISNADNAD(chain A and (resid 17 through 147 or (resid 148...AA - C17 - 50137
21HISHISLEULEU(chain B and (resid 17 through 232 or (resid 233...BB17 - 23237 - 252
22GLUGLUALAALA(chain B and (resid 17 through 232 or (resid 233...BB233 - 234253 - 254
23HISHISNADNAD(chain B and (resid 17 through 232 or (resid 233...BB - D17 - 50137
24HISHISNADNAD(chain B and (resid 17 through 232 or (resid 233...BB - D17 - 50137
25HISHISNADNAD(chain B and (resid 17 through 232 or (resid 233...BB - D17 - 50137
26GLNGLNGLNGLN(chain B and (resid 17 through 232 or (resid 233...BB255275
27GLNGLNGLNGLN(chain B and (resid 17 through 232 or (resid 233...BB255275
28HISHISNADNAD(chain B and (resid 17 through 232 or (resid 233...BB - D17 - 50137
29HISHISNADNAD(chain B and (resid 17 through 232 or (resid 233...BB - D17 - 50137
210HISHISNADNAD(chain B and (resid 17 through 232 or (resid 233...BB - D17 - 50137
211HISHISNADNAD(chain B and (resid 17 through 232 or (resid 233...BB - D17 - 50137

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Components

#1: Protein McyI-NAD


Mass: 38961.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena sp. 90 (bacteria) / Production host: Escherichia coli (E. coli)
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris-HCl, pH 8.5, and 20% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 17029 / % possible obs: 99.6 % / Redundancy: 6.5 % / CC1/2: 0.992 / Net I/σ(I): 16.9
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1700 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WWK

1wwk


Resolution: 2.8→48.482 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2456 806 4.87 %
Rwork0.1945 15732 -
obs0.197 16538 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 193.95 Å2 / Biso mean: 56.7813 Å2 / Biso min: 17.91 Å2
Refinement stepCycle: final / Resolution: 2.8→48.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4793 0 88 95 4976
Biso mean--33.07 34.66 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054973
X-RAY DIFFRACTIONf_angle_d0.8916782
X-RAY DIFFRACTIONf_chiral_restr0.055826
X-RAY DIFFRACTIONf_plane_restr0.005853
X-RAY DIFFRACTIONf_dihedral_angle_d19.3321804
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2852X-RAY DIFFRACTION13.546TORSIONAL
12B2852X-RAY DIFFRACTION13.546TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8001-2.97550.32521400.2669223784
2.9755-3.20520.29841240.24592693100
3.2052-3.52770.29421370.23762727100
3.5277-4.0380.2561250.1923265098
4.038-5.08650.22881450.15452684100
5.0865-48.4820.1851350.16972741100
Refinement TLS params.Method: refined / Origin x: 59.7192 Å / Origin y: 48.3556 Å / Origin z: 55.4699 Å
111213212223313233
T0.2935 Å2-0.0043 Å2-0.0089 Å2-0.1993 Å2-0.0201 Å2--0.235 Å2
L0.9835 °2-0.1256 °20.0374 °2-1.2737 °2-0.6575 °2--1.6811 °2
S0.0094 Å °0.0695 Å °-0.1313 Å °-0.1142 Å °0.0348 Å °-0.0477 Å °0.2031 Å °0.0437 Å °-0.0326 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA17 - 501
2X-RAY DIFFRACTION1allB17 - 501
3X-RAY DIFFRACTION1allS1 - 97

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