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

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Basic information

Entry
Database: PDB / ID: 8hbb
TitleCrystal structure of Caenorhabditis elegans NMAD-1 in complex with ligand III
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: 3.09 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
B: DNA N6-methyl adenine demethylase
C: DNA N6-methyl adenine demethylase
D: DNA N6-methyl adenine demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,30013
Polymers132,8844
Non-polymers4179
Water1629
1
A: DNA N6-methyl adenine demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3474
Polymers33,2211
Non-polymers1263
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA N6-methyl adenine demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3664
Polymers33,2211
Non-polymers1453
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA N6-methyl adenine demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3113
Polymers33,2211
Non-polymers902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA N6-methyl adenine demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2762
Polymers33,2211
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)183.176, 75.328, 118.184
Angle α, β, γ (deg.)90.00, 113.19, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 33220.957 Da / Num. of mol.: 4 / Mutation: E109K, Q112K, Q114K
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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.82 Å3/Da / Density % sol: 61.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 20% PEG 4000, 100 mM Na Caco pH 5.6

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.05→50 Å / Num. obs: 35949 / % possible obs: 90.9 % / Redundancy: 5.8 % / CC1/2: 0.959 / Net I/σ(I): 14.84
Reflection shellResolution: 3.05→3.15 Å / Num. unique obs: 26900 / CC1/2: 0.959

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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: 3.09→47.18 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 0.13 / Phase error: 28.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2818 1768 4.92 %
Rwork0.2595 --
obs0.2606 35949 67.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.09→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7679 0 5 9 7693
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0127827
X-RAY DIFFRACTIONf_angle_d1.65710630
X-RAY DIFFRACTIONf_dihedral_angle_d26.9912739
X-RAY DIFFRACTIONf_chiral_restr0.1251199
X-RAY DIFFRACTIONf_plane_restr0.0051383
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.09-3.180.3844550.31331253X-RAY DIFFRACTION32
3.18-3.270.3979820.29881551X-RAY DIFFRACTION40
3.27-3.380.2989820.31131712X-RAY DIFFRACTION45
3.38-3.50.36081100.28512020X-RAY DIFFRACTION52
3.5-3.640.33121200.28212162X-RAY DIFFRACTION56
3.64-3.80.28641390.28142463X-RAY DIFFRACTION63
3.8-40.34391130.2662704X-RAY DIFFRACTION70
4-4.250.25731620.24472947X-RAY DIFFRACTION76
4.25-4.580.27421510.24383120X-RAY DIFFRACTION81
4.58-5.040.24712000.24163378X-RAY DIFFRACTION88
5.04-5.770.29831880.26923580X-RAY DIFFRACTION92
5.77-7.260.31951750.27753676X-RAY DIFFRACTION95
7.26-47.180.2151910.22823615X-RAY DIFFRACTION93

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