[English] 日本語
Yorodumi
- PDB-7cy7: Crystal Structure of CMD1 in complex with DNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cy7
TitleCrystal Structure of CMD1 in complex with DNA
Components
  • DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')
  • Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1
KeywordsTRANSFERASE / TET / Vitamin C / dioxygenase / 5gmC / DNA modification / 2-oxoglutarate
Function / homology
Function and homology information


methylcytosine to 5-glyceryl-methylcytosine dioxygenase activity / regulation of photosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / : / dioxygenase activity / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport ...methylcytosine to 5-glyceryl-methylcytosine dioxygenase activity / regulation of photosynthesis / Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous / : / dioxygenase activity / detection of maltose stimulus / maltose transport complex / maltose binding / carbohydrate transport / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / iron ion binding / DNA damage response / membrane / nucleus
Similarity search - Function
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
: / ISOPROPYL ALCOHOL / DNA / DNA (> 10) / 5-methylcytosine-modifying enzyme 1 / Maltodextrin-binding protein / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Chlamydomonas reinhardtii (plant)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsLi, W. / Zhang, T. / Sun, M. / Ding, J.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31530013 China
National Natural Science Foundation of China (NSFC)31800622 China
Chinese Academy of SciencesXDB37030305 China
CitationJournal: Nat Commun / Year: 2021
Title: Molecular mechanism for vitamin C-derived C 5 -glyceryl-methylcytosine DNA modification catalyzed by algal TET homologue CMD1.
Authors: Li, W. / Zhang, T. / Sun, M. / Shi, Y. / Zhang, X.J. / Xu, G.L. / Ding, J.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1
C: DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')
D: DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,12113
Polymers107,5093
Non-polymers61210
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint8 kcal/mol
Surface area36780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.613, 125.764, 64.034
Angle α, β, γ (deg.)90.000, 102.820, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein / DNA chain , 2 types, 3 molecules ACD

#1: Protein Maltodextrin-binding protein,5-methylcytosine-modifying enzyme 1 / 5mC-modifying enzyme 1 / Ten-eleven translocation 1 gene protein homolog / CrTET1


Mass: 98913.453 Da / Num. of mol.: 1 / Mutation: D108A, K109A, E198A, N199A, E385A, K388A, D389A
Source method: isolated from a genetically manipulated source
Details: The fusion protein of Maltodextrin-binding protein UNP RESIDUES 27-392), linker, 5-methylcytosine-modifying enzyme 1 (UNP RESIDUES 1-532) and tags
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Chlamydomonas reinhardtii (plant)
Gene: CMD1, CHLRE_12g553400v5 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A376KDN7, UniProt: A0A2K3D5Z7, UniProt: P0AEX9*PLUS, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; Miscellaneous
#2: DNA chain DNA (5'-D(P*CP*GP*CP*GP*CP*GP*GP*GP*A)-3')


Mass: 4297.778 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 4 types, 412 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Feature type: SUBJECT OF INVESTIGATION / Comment: alkaloid*YM
#5: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 15% (v/v) 2-propanol, 0.1 M sodium citrate, pH 5.0, and 10% (w/v) PEG 10000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.15→50.01 Å / Num. obs: 60566 / % possible obs: 96.7 % / Redundancy: 6.6 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.8
Reflection shellResolution: 2.15→2.21 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2 / Num. unique obs: 3028 / CC1/2: 0.82

-
Processing

Software
NameVersionClassification
XDSdata scaling
REFMAC5.8.0155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CY4

7cy4


Resolution: 2.15→50.01 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 11.678 / SU ML: 0.131 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2206 3035 5 %RANDOM
Rwork0.1879 ---
obs0.1896 57529 94.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 189.11 Å2 / Biso mean: 40.4 Å2 / Biso min: 12.18 Å2
Baniso -1Baniso -2Baniso -3
1-2.87 Å2-0 Å2-0.62 Å2
2---3.82 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 2.15→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6624 327 37 402 7390
Biso mean--53.57 37.78 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197185
X-RAY DIFFRACTIONr_bond_other_d0.0020.026697
X-RAY DIFFRACTIONr_angle_refined_deg1.1181.9089815
X-RAY DIFFRACTIONr_angle_other_deg0.993315407
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5965876
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81524.533289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.943151090
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4791535
X-RAY DIFFRACTIONr_chiral_restr0.0550.21076
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218022
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021628
X-RAY DIFFRACTIONr_rigid_bond_restr3.986313881
X-RAY DIFFRACTIONr_sphericity_free26.6095124
X-RAY DIFFRACTIONr_sphericity_bonded20.093513981
LS refinement shellResolution: 2.15→2.206 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 163 -
Rwork0.288 2825 -
all-2988 -
obs--62.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0451-0.00630.03850.0023-0.00220.04830.0047-0.0022-0.00130.0025-0.0028-0.0009-0.0048-0.0072-0.00190.04540.00360.01890.13830.00020.088467.465817.6997147.9492
20.8295-2.4629-0.64167.3371.9250.51770.0260.0259-0.1199-0.1577-0.09940.3662-0.0839-0.04050.07340.15090.04270.03230.09890.0080.0921478.357438.431146.9184
30.6365-0.98520.01071.5262-0.01650.0044-0.0416-0.03290.05340.0640.039-0.0896-0.0199-0.00220.00260.09460.0234-0.03090.1578-0.01530.117480.275934.4643149.203
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-371 - 507
2X-RAY DIFFRACTION2C3 - 11
3X-RAY DIFFRACTION3D1 - 7

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more