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- PDB-8h68: Crystal structure of Caenorhabditis elegans NMAD-1 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 8h68
TitleCrystal structure of Caenorhabditis elegans NMAD-1 in complex with NOG and Mg(II)
ComponentsMaltose/maltodextrin-binding periplasmic protein,DNA N6-methyl adenine demethylase
KeywordsMETAL BINDING PROTEIN / 2-OG/Fe dependent
Function / homology
Function and homology information


DNA N6-methyladenine demethylase activity / DNA N6-methyladenine demethylase / positive regulation of egg-laying behavior / positive regulation of fertilization / meiotic chromosome condensation / contractile ring / positive regulation of chromosome organization / demethylation / positive regulation of meiosis I / broad specificity oxidative DNA demethylase activity ...DNA N6-methyladenine demethylase activity / DNA N6-methyladenine demethylase / positive regulation of egg-laying behavior / positive regulation of fertilization / meiotic chromosome condensation / contractile ring / positive regulation of chromosome organization / demethylation / positive regulation of meiosis I / broad specificity oxidative DNA demethylase activity / demethylase activity / actomyosin structure organization / positive regulation of double-strand break repair / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / actin binding / outer membrane-bounded periplasmic space / midbody / DNA replication / oxidoreductase activity / metal ion binding / nucleus
Similarity search - Function
Alpha-ketoglutarate-dependent dioxygenase alkB homologue 4 / Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
alpha-maltotetraose / GLYCINE / N-OXALYLGLYCINE / DI(HYDROXYETHYL)ETHER / Maltose/maltodextrin-binding periplasmic protein / DNA N6-methyl adenine demethylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Caenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsShi, Y. / Ding, J. / Yang, H.
Funding support2items
OrganizationGrant numberCountry
Other government2020YFA0803200
Other government2020YFA0509000
CitationJournal: J Mol Cell Biol / Year: 2023
Title: Caenorhabditis elegans NMAD-1 functions as a demethylase for actin.
Authors: Shi, Y. / Yang, H. / Ding, J.
History
DepositionOct 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,DNA N6-methyl adenine demethylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,3338
Polymers70,9531
Non-polymers1,3807
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.026, 91.867, 133.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Maltose/maltodextrin-binding periplasmic protein,DNA N6-methyl adenine demethylase / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / N6-methyl adenine demethylase 1


Mass: 70953.328 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Caenorhabditis elegans (invertebrata)
Gene: malE, Z5632, ECs5017, nmad-1, F09F7.7 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: Q8MNT9, DNA N6-methyladenine demethylase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltotetraose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1a_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}LINUCSPDB-CARE

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Non-polymers , 7 types, 203 molecules

#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#5: Chemical ChemComp-OGA / N-OXALYLGLYCINE / N-Oxalylglycine


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M HEPES, pH 7.5, 10% (w/v) PEG 6000, 10% (v/v) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.01→75.64 Å / Num. obs: 31436 / % possible obs: 98.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 38.35 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.059 / Rrim(I) all: 0.108 / Net I/σ(I): 8.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.01-2.063.41.1821011230170.5440.7591.4110.999.8
8.99-75.642.80.03114455110.9960.0210.03828.995

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RZL

3rzl


Resolution: 2.2→46.84 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.242 3557 6.34 %
Rwork0.1819 --
obs0.1856 31430 93.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→46.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4901 0 91 197 5189
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095113
X-RAY DIFFRACTIONf_angle_d0.9426927
X-RAY DIFFRACTIONf_dihedral_angle_d9.931697
X-RAY DIFFRACTIONf_chiral_restr0.054761
X-RAY DIFFRACTIONf_plane_restr0.007883
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.32661450.27522138X-RAY DIFFRACTION94
2.23-2.260.3451440.27582098X-RAY DIFFRACTION93
2.26-2.30.3291390.25921996X-RAY DIFFRACTION89
2.3-2.330.31711250.26151900X-RAY DIFFRACTION85
2.33-2.370.29061500.25882203X-RAY DIFFRACTION96
2.37-2.410.25821500.25242159X-RAY DIFFRACTION96
2.41-2.450.28941450.25032146X-RAY DIFFRACTION96
2.45-2.50.361390.23342201X-RAY DIFFRACTION96
2.5-2.550.36131430.23372128X-RAY DIFFRACTION95
2.55-2.610.25651420.22472190X-RAY DIFFRACTION95
2.61-2.670.27741460.21962092X-RAY DIFFRACTION94
2.67-2.740.26151430.2152124X-RAY DIFFRACTION94
2.74-2.810.25311370.22881969X-RAY DIFFRACTION88
2.81-2.890.26261410.21262049X-RAY DIFFRACTION91
2.89-2.990.28641490.21122192X-RAY DIFFRACTION96
2.99-3.090.27461510.20652148X-RAY DIFFRACTION96
3.09-3.220.27731500.19782143X-RAY DIFFRACTION96
3.22-3.360.24861430.17842166X-RAY DIFFRACTION95
3.36-3.540.25321370.17572141X-RAY DIFFRACTION94
3.54-3.760.21691310.15761938X-RAY DIFFRACTION86
3.76-4.050.19541400.14512136X-RAY DIFFRACTION95
4.05-4.460.19611550.13022101X-RAY DIFFRACTION93
4.46-5.10.18681440.12472098X-RAY DIFFRACTION93
5.1-6.430.21581340.15782052X-RAY DIFFRACTION90
6.43-46.840.18021340.1492072X-RAY DIFFRACTION92
Refinement TLS params.Method: refined / Origin x: 22.085 Å / Origin y: -32.3095 Å / Origin z: -19.4773 Å
111213212223313233
T0.2249 Å2-0.0253 Å20.0491 Å2-0.3079 Å2-0.0144 Å2--0.2319 Å2
L0.269 °2-0.2412 °20.2524 °2-1.803 °2-0.4939 °2--0.5884 °2
S0.0487 Å °-0.0278 Å °-0.0238 Å °0.1545 Å °-0.0562 Å °0.0867 Å °0.0192 Å °-0.021 Å °0.0043 Å °
Refinement TLS groupSelection details: all

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