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- PDB-8wpq: Anabaena McyI R166M with prebound NAD and citrate -

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Basic information

Entry
Database: PDB / ID: 8wpq
TitleAnabaena McyI R166M with prebound NAD and citrate
ComponentsMcyI
KeywordsOXIDOREDUCTASE / hepatotoxin / microcystin / cofactor / Anabaena
Function / homologyCITRATE ANION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesAnabaena sp. 90 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7883
Polymers38,9361
Non-polymers8532
Water1,45981
1
A: McyI
hetero molecules

A: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5776
Polymers77,8722
Non-polymers1,7054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8670 Å2
ΔGint-29 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.186, 61.186, 173.858
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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-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
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 47.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M AmSO4, 0.1 M tri-Sodium citrate , pH 5.6, 15% (w/v) PEG 4000

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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: Jan 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 12233 / % possible obs: 99.5 % / Redundancy: 5.3 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.041 / Rrim(I) all: 0.097 / Χ2: 0.857 / Net I/σ(I): 6.1 / Num. measured all: 65120
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.6-2.695.30.7812060.7120.9120.3550.8620.63499.8
2.69-2.85.10.6111990.8040.9440.2870.6780.64299.3
2.8-2.935.40.43911910.9010.9740.20.4860.799.8
2.93-3.085.70.3212030.9240.980.1430.3530.74699.9
3.08-3.285.60.2311930.9580.9890.1040.2540.87699.8
3.28-3.535.30.16712140.9710.9930.0790.1861.06399.8
3.53-3.885.10.13512100.9810.9950.0650.1511.36298.8
3.88-4.455.50.08612300.990.9970.0390.0951.15699.4
4.45-5.65.10.06412500.9930.9980.030.0710.89599.4
5.6-505.10.03613370.99810.0180.0410.52398.9

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Processing

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

1wwk


Resolution: 2.6→29.07 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 661 5.78 %
Rwork0.2144 --
obs0.2173 11437 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2468 0 0 81 2549
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032532
X-RAY DIFFRACTIONf_angle_d0.593457
X-RAY DIFFRACTIONf_dihedral_angle_d15.361931
X-RAY DIFFRACTIONf_chiral_restr0.043416
X-RAY DIFFRACTIONf_plane_restr0.004439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.80.3214860.2841609X-RAY DIFFRACTION70
2.8-3.080.32441520.25892214X-RAY DIFFRACTION99
3.08-3.530.30611110.24282290X-RAY DIFFRACTION100
3.53-4.440.2971360.2042280X-RAY DIFFRACTION98
4.44-29.070.20061760.17832383X-RAY DIFFRACTION99

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