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- PDB-8wpi: Anabaena McyI with prebound NAD and soaked NADP -

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Basic information

Entry
Database: PDB / ID: 8wpi
TitleAnabaena McyI with prebound NAD and soaked NADP
ComponentsMcyI
KeywordsOXIDOREDUCTASE / hepatotoxin / microcystin / cofactor / Anabaena
Function / homologyNICOTINAMIDE-ADENINE-DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesAnabaena sp. 90 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.201 Å
AuthorsWang, X. / Yin, Y. / Duan, Y. / Liu, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Anabaena McyI with prebound NAD and soaked NADP
Authors: Xiao, W. / Yue, Y. / Yafei, D.
History
DepositionOct 10, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2024Provider: 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)81,4817
Polymers77,9242
Non-polymers3,5575
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9260 Å2
ΔGint-51 kcal/mol
Surface area26090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.549, 74.549, 127.828
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 - C18 - 40138
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.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M trimethylamine N-oxide, 0.1 M Tris-HCl, pH 8.5, 20% (w/v) PEG 2000 MME, 15 mM NADP

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 35329 / % possible obs: 100 % / Redundancy: 13.6 % / CC1/2: 0.996 / Net I/σ(I): 27.5
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 3499 / CC1/2: 0.809

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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: 2.201→48.522 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2069 1725 4.89 %
Rwork0.176 33540 -
obs0.1775 35265 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 184.84 Å2 / Biso mean: 63.1212 Å2 / Biso min: 24.24 Å2
Refinement stepCycle: final / Resolution: 2.201→48.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 236 217 5313
Biso mean--57.16 56.81 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045200
X-RAY DIFFRACTIONf_angle_d0.797112
X-RAY DIFFRACTIONf_chiral_restr0.049850
X-RAY DIFFRACTIONf_plane_restr0.005876
X-RAY DIFFRACTIONf_dihedral_angle_d17.6091868
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2997X-RAY DIFFRACTION8.717TORSIONAL
12B2997X-RAY DIFFRACTION8.717TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2014-2.26620.2671470.24012762100
2.2662-2.33930.26791250.22922819100
2.3393-2.42290.29471570.22292767100
2.4229-2.51990.25721650.21742768100
2.5199-2.63460.21821370.19792798100
2.6346-2.77350.24091440.20082814100
2.7735-2.94720.23621490.19872768100
2.9472-3.17480.22761310.20152791100
3.1748-3.49420.20611590.18632787100
3.4942-3.99960.20341430.15982809100
3.9996-5.03820.15271220.14062848100
5.0382-48.5220.18871460.1604280999
Refinement TLS params.Method: refined / Origin x: -24.8358 Å / Origin y: -14.8364 Å / Origin z: 6.6906 Å
111213212223313233
T0.2694 Å2-0.0421 Å20.0264 Å2-0.3113 Å20.0125 Å2--0.2479 Å2
L1.9949 °2-0.7778 °20.4275 °2-1.5733 °2-0.0206 °2--1.7026 °2
S-0.0027 Å °0.0439 Å °-0.174 Å °0.0764 Å °0.0293 Å °0.2782 Å °-0.0568 Å °-0.2218 Å °-0.0281 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA18 - 401
2X-RAY DIFFRACTION1allA402
3X-RAY DIFFRACTION1allA403
4X-RAY DIFFRACTION1allA403
5X-RAY DIFFRACTION1allB18 - 335
6X-RAY DIFFRACTION1allB401
7X-RAY DIFFRACTION1allB402
8X-RAY DIFFRACTION1allS1 - 219

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