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- PDB-8wpj: Anabaena McyI with prebound NAD and soaked NAD -

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Basic information

Entry
Database: PDB / ID: 8wpj
TitleAnabaena McyI with prebound NAD and soaked NAD
ComponentsMcyI
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
B: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5786
Polymers77,9242
Non-polymers2,6544
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-46 kcal/mol
Surface area26940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.050, 75.050, 127.305
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
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1NADNADchain AAA - D18 - 40238
2TRPTRPchain BBB18 - 33538 - 355

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Components

#1: Protein McyI


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.: 4 / 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.: 6 / 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: 2.3 Å3/Da / Density % sol: 46.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 200 mM trimethylamine N-oxide, 100 mM Tris HCl, pH 8.5, 20% PEG 2000 MME, 15 mM NAD

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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 29, 2020
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: 17359 / % possible obs: 99.6 % / Redundancy: 5.4 % / CC1/2: 0.984 / Net I/σ(I): 14.3
Reflection shellResolution: 2.8→2.9 Å / Num. unique obs: 1736 / CC1/2: 0.675

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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→48.983 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2534 896 5.17 %
Rwork0.2002 16426 -
obs0.2029 17322 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 242.44 Å2 / Biso mean: 86.3775 Å2 / Biso min: 37.24 Å2
Refinement stepCycle: final / Resolution: 2.8→48.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 176 6 5042
Biso mean--81.51 67.74 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035138
X-RAY DIFFRACTIONf_angle_d0.6727016
X-RAY DIFFRACTIONf_chiral_restr0.045842
X-RAY DIFFRACTIONf_plane_restr0.005872
X-RAY DIFFRACTIONf_dihedral_angle_d12.7093052
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2985X-RAY DIFFRACTION7.422TORSIONAL
12B2985X-RAY DIFFRACTION7.422TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8-2.97530.31421240.28422750100
2.9753-3.2050.31751500.2742273799
3.205-3.52740.33191680.24292702100
3.5274-4.03770.27311420.21492750100
4.0377-5.08620.21411690.16712721100
5.0862-48.9830.22081430.1733276699
Refinement TLS params.Method: refined / Origin x: 14.6078 Å / Origin y: 25.8472 Å / Origin z: -6.1331 Å
111213212223313233
T0.4779 Å2-0.0347 Å20.0265 Å2-0.4534 Å20.0248 Å2--0.4521 Å2
L1.736 °2-0.8305 °20.1735 °2-2.0233 °20.2233 °2--1.9292 °2
S0.0029 Å °0.0897 Å °0.2527 Å °0.0481 Å °-0.0002 Å °-0.0575 Å °-0.1301 Å °-0.1003 Å °-0.0057 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA18 - 402
2X-RAY DIFFRACTION1allB18 - 335
3X-RAY DIFFRACTION1allB401
4X-RAY DIFFRACTION1allB402
5X-RAY DIFFRACTION1allS1 - 7

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