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- PDB-8haz: Crystal structure of Caenorhabditis elegans NMAD-1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8haz
TitleCrystal structure of Caenorhabditis elegans NMAD-1 in complex with ligand I
ComponentsDNA N6-methyl adenine demethylase
KeywordsOXIDOREDUCTASE / NMAD-1A / GENE REGULATION
Function / homology
Function and homology information


positive regulation of egg-laying behavior / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / positive regulation of fertilization / meiotic chromosome condensation / positive regulation of chromosome organization / demethylation / positive regulation of meiosis I / broad specificity oxidative DNA demethylase activity / demethylase activity ...positive regulation of egg-laying behavior / DNA N6-methyladenine demethylase / DNA N6-methyladenine demethylase activity / positive regulation of fertilization / meiotic chromosome condensation / positive regulation of chromosome organization / demethylation / positive regulation of meiosis I / broad specificity oxidative DNA demethylase activity / demethylase activity / positive regulation of double-strand break repair / DNA replication / oxidoreductase activity / nucleus / metal ion binding
Similarity search - Function
Alpha-ketoglutarate-dependent dioxygenase alkB homologue 4 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily
Similarity search - Domain/homology
DNA N6-methyl adenine demethylase
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.66 Å
AuthorsShang, G. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int J Mol Sci / Year: 2024
Title: Structural Basis of Nucleic Acid Recognition and 6mA Demethylation by Caenorhabditis elegans NMAD-1A.
Authors: Shang, G. / Yang, M. / Li, M. / Ma, L. / Liu, Y. / Ma, J. / Chen, Y. / Wang, X. / Fan, S. / Xie, M. / Wu, W. / Dai, S. / Chen, Z.
History
DepositionOct 27, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA N6-methyl adenine demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6132
Polymers28,5171
Non-polymers961
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 111
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.221, 48.528, 51.878
Angle α, β, γ (deg.)90.00, 104.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DNA N6-methyl adenine demethylase / N6-methyl adenine demethylase 1


Mass: 28516.553 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: nmad-1, F09F7.7 / Production host: prokaryote coculture (bacteria)
References: UniProt: Q8MNT9, DNA N6-methyladenine demethylase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% PEG 3350, 200 mM, CH3COONH4, 100 mM Bis-Tris pH 6.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 6106 / % possible obs: 90.3 % / Redundancy: 3.4 % / CC1/2: 0.965 / Net I/σ(I): 9.7
Reflection shellResolution: 2.65→2.7 Å / Num. unique obs: 597 / CC1/2: 0.894

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.66→37.54 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2731 264 5.01 %
Rwork0.2493 --
obs0.2504 5265 83.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.66→37.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1725 0 0 73 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091757
X-RAY DIFFRACTIONf_angle_d0.9892370
X-RAY DIFFRACTIONf_dihedral_angle_d25.056653
X-RAY DIFFRACTIONf_chiral_restr0.063257
X-RAY DIFFRACTIONf_plane_restr0.004304
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.750.31351330.3022322X-RAY DIFFRACTION79
3.35-37.540.25591310.22942679X-RAY DIFFRACTION89

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