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- PDB-8wpr: Anabaena McyI R166A with prebound NAD and malate -

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Basic information

Entry
Database: PDB / ID: 8wpr
TitleAnabaena McyI R166A 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: 1.7 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)39,7654
Polymers38,8761
Non-polymers8903
Water6,053336
1
A: McyI
hetero molecules

A: McyI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5318
Polymers77,7522
Non-polymers1,7796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7960 Å2
ΔGint-32 kcal/mol
Surface area25250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.172, 61.172, 173.602
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-599-

HOH

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Components

#1: Protein McyI


Mass: 38875.832 Da / Num. of mol.: 1 / Mutation: R166A
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
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: 1.7→50 Å / Num. obs: 42382 / % possible obs: 99.7 % / Redundancy: 18 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.029 / Rrim(I) all: 0.119 / Χ2: 1.869 / Net I/σ(I): 6.4 / Num. measured all: 761880
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.7-1.7613.50.95440170.8180.9490.2630.9920.95897.6
1.76-1.8318.60.6742010.9330.9830.1580.6891.02299.9
1.83-1.9119.80.50141940.9620.990.1150.5141.154100
1.91-2.0219.20.34941670.9790.9950.0810.3591.355100
2.02-2.1418.70.2442300.9880.9970.0570.2461.642100
2.14-2.3119.50.18642070.9930.9980.0430.1911.891100
2.31-2.5418.10.14342390.9950.9990.0350.1472.126100
2.54-2.9119.10.11642700.9970.9990.0270.122.455100
2.91-3.6617.60.09243140.9970.9990.0230.0952.92100
3.66-5015.70.07645430.9980.9990.020.0793.06399.8

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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: 1.7→45.22 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1777 2051 4.85 %
Rwork0.1644 --
obs0.165 42311 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2482 0 15 336 2833
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062612
X-RAY DIFFRACTIONf_angle_d1.0053574
X-RAY DIFFRACTIONf_dihedral_angle_d16.939976
X-RAY DIFFRACTIONf_chiral_restr0.062428
X-RAY DIFFRACTIONf_plane_restr0.006455
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.740.25521350.22742523X-RAY DIFFRACTION97
1.74-1.780.2191440.20652631X-RAY DIFFRACTION99
1.78-1.830.20561300.19032657X-RAY DIFFRACTION100
1.83-1.880.2161480.18682637X-RAY DIFFRACTION100
1.89-1.950.22451320.19272640X-RAY DIFFRACTION100
1.95-2.020.18911290.17322665X-RAY DIFFRACTION100
2.02-2.10.23131340.17082671X-RAY DIFFRACTION100
2.1-2.190.22311290.17132695X-RAY DIFFRACTION100
2.19-2.310.2011140.16652686X-RAY DIFFRACTION100
2.31-2.450.19881310.17492706X-RAY DIFFRACTION100
2.45-2.640.19061370.17182678X-RAY DIFFRACTION100
2.64-2.910.18861540.1772694X-RAY DIFFRACTION100
2.91-3.330.17341600.16732692X-RAY DIFFRACTION100
3.33-4.190.16671490.14912752X-RAY DIFFRACTION100
4.19-45.220.11971250.1422933X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 14.7413 Å / Origin y: -8.2637 Å / Origin z: -4.5544 Å
111213212223313233
T0.2282 Å20.0031 Å2-0.0113 Å2-0.148 Å20.0462 Å2--0.1994 Å2
L0.679 °2-0.3494 °2-0.0355 °2-0.7674 °20.6147 °2--0.9783 °2
S0.0737 Å °-0.0238 Å °-0.0997 Å °-0.1101 Å °-0.0273 Å °-0.0084 Å °0.1231 Å °0.0702 Å °-0.0425 Å °
Refinement TLS groupSelection details: all

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