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- PDB-7vpn: Crystal Structure of the dioxygenase CcTet from Coprinopsis ciner... -

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Basic information

Entry
Database: PDB / ID: 7vpn
TitleCrystal Structure of the dioxygenase CcTet from Coprinopsis cinereain in complex with Mn(II) and N-Oxalylglycine
ComponentsCcTet molecule
KeywordsDNA BINDING PROTEIN / dioxygenase / 5-methylcytosine oxidation / N6-methyldeoxyadenine demethylation
Function / homology2OGFeDO, oxygenase domain / Oxygenase domain of the 2OGFeDO superfamily / dioxygenase activity / metal ion binding / : / N-OXALYLGLYCINE / 2OGFeDO JBP1/TET oxygenase domain-containing protein
Function and homology information
Biological speciesCoprinopsis cinerea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMu, Y.J. / Zhang, L. / Zhang, L.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)91853118 China
National Natural Science Foundation of China (NSFC)22107067 China
National Natural Science Foundation of China (NSFC)22077081 China
National Natural Science Foundation of China (NSFC)21722802 China
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: A fungal dioxygenase CcTet serves as a eukaryotic 6mA demethylase on duplex DNA.
Authors: Mu, Y. / Zhang, L. / Hu, J. / Zhou, J. / Lin, H.W. / He, C. / Chen, H.Z. / Zhang, L.
History
DepositionOct 17, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 6, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CcTet molecule
B: CcTet molecule
C: CcTet molecule
D: CcTet molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,8399
Polymers192,4724
Non-polymers3675
Water3,693205
1
A: CcTet molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3203
Polymers48,1181
Non-polymers2022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CcTet molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1732
Polymers48,1181
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CcTet molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1732
Polymers48,1181
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: CcTet molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1732
Polymers48,1181
Non-polymers551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)219.804, 219.804, 77.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number172
Space group name H-MP64

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Components

#1: Protein
CcTet molecule


Mass: 48117.977 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coprinopsis cinerea (strain Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003) (fungus)
Strain: Okayama-7 / 130 / ATCC MYA-4618 / FGSC 9003 / Gene: CC1G_05589 / Production host: Escherichia coli (E. coli) / References: UniProt: A8P1J0
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 56.34 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 20 mM Sodium formate, 10% PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 13, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 66088 / % possible obs: 100 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.304 / Rpim(I) all: 0.094 / Rrim(I) all: 0.319 / Χ2: 0.979 / Net I/σ(I): 5 / Num. measured all: 757847
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.6-2.6411.82.20532740.4150.6682.3050.929
2.64-2.6911.81.66932590.5650.5061.7450.92
2.69-2.7411.81.41833180.6520.4311.4830.925
2.74-2.811.71.08932840.7570.3321.1390.945
2.8-2.8611.60.9232980.8040.2810.9620.957
2.86-2.9311.40.75332360.8490.2320.7880.963
2.93-311.30.64533010.8920.1990.6750.962
3-3.0810.80.52132680.9080.1660.5470.951
3.08-3.1710.60.44432950.9330.1410.4660.96
3.17-3.2811.80.39333130.9380.1180.4110.987
3.28-3.3911.80.35632720.9480.1070.3721.001
3.39-3.5311.70.32433200.9530.0980.3391
3.53-3.6911.70.30432920.9530.0920.3181.001
3.69-3.8811.50.29233320.9440.090.3060.989
3.88-4.1310.60.2832630.9480.090.2950.972
4.13-4.4511.80.28332850.9550.0850.2960.985
4.45-4.8911.90.27733640.9570.0830.2891.01
4.89-5.611.50.27633150.9450.0840.2890.987
5.6-7.05110.27433590.950.0850.2881.001
7.05-5011.20.29234400.940.0910.3061.137

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NM6

4nm6


Resolution: 2.6→49.16 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2662 3120 5.17 %
Rwork0.2171 57224 -
obs0.2196 60344 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 178.63 Å2 / Biso mean: 61.5826 Å2 / Biso min: 13.78 Å2
Refinement stepCycle: final / Resolution: 2.6→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10884 0 14 205 11103
Biso mean--38.61 42.53 -
Num. residues----1388
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.640.3873210.367434336412
2.64-2.690.3762690.32181346141548
2.69-2.730.34691220.30552305242782
2.73-2.780.31871610.27232662282393
2.78-2.840.30721770.26462651282896
2.84-2.890.30071620.25542783294598
2.89-2.960.31931600.26222774293499
2.96-3.020.31441610.26032822298399
3.02-3.10.32191480.24552803295199
3.1-3.180.30211470.25292779292699
3.18-3.280.28141300.23272863299399
3.28-3.380.3261390.23122828296799
3.38-3.50.26061720.2352767293998
3.5-3.640.29861340.22642809294398
3.65-3.810.26691380.21242821295998
3.81-4.010.23841390.20332811295099
4.01-4.260.24461610.19742811297299
4.26-4.590.24681490.1852843299299
4.59-5.050.21981670.17892805297299
5.05-5.780.22411590.204228713030100
5.78-7.280.25841760.20772862303899
7.29-49.160.20651280.17382865299396

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