[English] 日本語
Yorodumi
- PDB-4rtn: Complex of Escherichia coli DNA Adenine Methyltransferase (DAM) w... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rtn
TitleComplex of Escherichia coli DNA Adenine Methyltransferase (DAM) with AdoHcy and with DNA Containing Proximal Pap Regulon Sequence
Components
  • DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*A)-3')
  • DNA (5'-D(*TP*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3')
  • DNA adenine methylase
KeywordsTransferase/DNA / DAM METHYLATION / GATC RECOGNITION / BASE FLIPPING / BACTERIAL VIRULENCE / methylation-independent transcriptional repressor / Transferase-DNA complex
Function / homology
Function and homology information


bacterial-type DNA replication initiation / : / site-specific DNA-methyltransferase (adenine-specific) / site-specific DNA-methyltransferase (adenine-specific) activity / S-adenosyl-L-methionine binding / mismatch repair / response to UV / DNA-templated DNA replication / sequence-specific DNA binding
Similarity search - Function
Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily ...Adenine-specific Methyltransferase; domain 2 / Adenine-specific Methyltransferase, Domain 2 / Adenine modification methylase, M.EcoRV-type / D12 class N6 adenine-specific DNA methyltransferase / Adenine-specific methyltransferase, domain 2 / D12 class N6 adenine-specific DNA methyltransferase / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / DNA / DNA (> 10) / : / DNA adenine methylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsHorton, J.R. / Cheng, X.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structures of Escherichia coli DNA adenine methyltransferase (Dam) in complex with a non-GATC sequence: potential implications for methylation-independent transcriptional repression.
Authors: Horton, J.R. / Zhang, X. / Blumenthal, R.M. / Cheng, X.
History
DepositionNov 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 20, 2015Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA adenine methylase
F: DNA (5'-D(*TP*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3')
G: DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4204
Polymers41,0353
Non-polymers3841
Water61334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.201, 63.477, 144.048
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein DNA adenine methylase /


Mass: 34330.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. MDS42 / Gene: dam, ECMDS42_2833 / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: H0Q7C9, UniProt: P0AEE8*PLUS
#2: DNA chain DNA (5'-D(*TP*TP*TP*AP*AP*AP*GP*AP*TP*CP*G)-3')


Mass: 3372.234 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*CP*GP*AP*TP*CP*TP*TP*TP*AP*A)-3')


Mass: 3332.210 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHOR STATES THAT RESIDUES 175 WERE MODELED AS SER INSTEAD OF ALA BECAUSE OF EXTRA DENSITY.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 24% PEG200, 100mM KCl, 10mM MgSO4, 100mM HEPES buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 15, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.59→29.044 Å / Num. all: 10911 / Num. obs: 10911 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 42.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12
Reflection shellResolution: 2.59→2.68 Å / Redundancy: 9 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 4.8 / Num. unique all: 1049 / % possible all: 100

-
Processing

Software
NameVersionClassification
SERGUIdata collection
GLRFphasing
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G1P

2g1p


Resolution: 2.59→29 Å / SU ML: 0.26 / σ(F): 1.33 / Phase error: 25.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2396 566 5.21 %RANDOM
Rwork0.2051 ---
obs0.2069 10863 99.84 %-
all-10863 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 445 26 34 2472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032577
X-RAY DIFFRACTIONf_angle_d0.5983603
X-RAY DIFFRACTIONf_dihedral_angle_d17.824945
X-RAY DIFFRACTIONf_chiral_restr0.026390
X-RAY DIFFRACTIONf_plane_restr0.003389
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.85320.32161320.27392502X-RAY DIFFRACTION100
2.8532-3.26560.25211380.25392536X-RAY DIFFRACTION100
3.2656-4.11240.24841430.19322563X-RAY DIFFRACTION100
4.1124-29.04540.20591530.1762696X-RAY DIFFRACTION100
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)
10.8686-0.6561-0.19471.47570.08220.69680.14930.1254-0.2419-0.1531-0.02470.43250.158-0.22710.00040.3256-0.0183-0.12430.28960.00840.379-10.3352-5.111993.7697
21.246-0.14890.5541.2852-0.16311.0795-0.0301-0.11390.24310.25110.06290.0485-0.167-0.0666-00.26320.03010.020.2688-0.00750.2463-3.447512.2195104.6998
32.5979-0.6851.24761.0801-0.71761.50870.52990.5545-0.6503-0.4096-0.30360.30830.53880.21610.04190.47090.116-0.1160.3427-0.11960.3341-4.9641-7.722784.0089
40.1072-0.1498-0.0030.459-0.26410.1849-0.62320.88990.5958-0.11220.1216-0.16190.0468-0.0331-0.04560.3778-0.07160.03090.67430.10420.503320.088218.671485.9866
50.2825-0.4791-0.31140.78250.02380.8229-0.23050.8335-0.0889-0.19180.056-0.0891-0.04990.1485-0.00020.4904-0.01880.02230.64920.06210.690317.27818.51186.161
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:68 )A3 - 68
2X-RAY DIFFRACTION2( CHAIN A AND RESID 69:144 )A69 - 144
3X-RAY DIFFRACTION3( CHAIN A AND RESID 145:270 )A145 - 270
4X-RAY DIFFRACTION4( CHAIN F AND RESID 1:11 )F1 - 11
5X-RAY DIFFRACTION5( CHAIN G AND RESID 1:11 )G1 - 11

+
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