[English] 日本語
Yorodumi
- PDB-3mx1: The structure of GIY-YIG endonuclease R.Eco29kI -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mx1
TitleThe structure of GIY-YIG endonuclease R.Eco29kI
ComponentsEco29kIR
KeywordsHYDROLASE / type II restriction endonuclease / GIY-YIG endonuclease
Function / homologyRestriction endonuclease, type II, Eco29kI / Eco29kI restriction endonuclease / identical protein binding / Eco29kIR
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsMak, A.N.S. / Lambert, A.R. / Stoddard, B.L.
Citation
Journal: Structure / Year: 2010
Title: Folding, DNA Recognition, and Function of GIY-YIG Endonucleases: Crystal Structures of R.Eco29kI.
Authors: Mak, A.N. / Lambert, A.R. / Stoddard, B.L.
#1: Journal: Nucleic Acids Res. / Year: 1992
Title: Eco29kI, a novel plasmid encoded restriction endonuclease from Escherichia coli.
Authors: Pertzev, A.V. / Ruban, N.M. / Zakharova, M.V. / Beletzkaja, I.V. / Petrov, S.I. / Kravetz, A.N. / Solonin, A.S.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Eco29kIR


Theoretical massNumber of molelcules
Total (without water)26,7931
Polymers26,7931
Non-polymers00
Water3,063170
1
A: Eco29kIR

A: Eco29kIR


Theoretical massNumber of molelcules
Total (without water)53,5862
Polymers53,5862
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area3410 Å2
ΔGint-22 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.906, 90.074, 88.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Eco29kIR / Restriction endonuclease


Mass: 26792.988 Da / Num. of mol.: 1 / Mutation: E142Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: eco29kIR / Plasmid: pET-15HE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS
References: UniProt: Q46944, type II site-specific deoxyribonuclease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris HCl, 1.5M NaCl, 10% ethanol v/v, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.111
SYNCHROTRONALS 5.0.220.9801, 0.9802, 0.975
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 29, 2009
ADSC QUANTUM 3152CCDOct 28, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1single crystalSINGLE WAVELENGTHMx-ray1
2single crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.98011
30.98021
40.9751
ReflectionResolution: 2.3→62.91 Å / Num. all: 15893 / Num. obs: 15078 / % possible obs: 98.82 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 18.35
Reflection shellResolution: 2.3→2.358 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.311 / Mean I/σ(I) obs: 4.2 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.5.0088refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD
Starting model: Phase information by PHENIX

Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.695 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22781 791 5 %RANDOM
Rwork0.18285 ---
obs0.18507 15078 98.82 %-
all-15893 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.06 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20 Å2
2--1.97 Å20 Å2
3----2.59 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 0 170 1810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0211689
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9511.9282285
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6595207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55722.38184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.52215256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8271514
X-RAY DIFFRACTIONr_chiral_restr0.1390.2226
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211342
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2791.51023
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.34621630
X-RAY DIFFRACTIONr_scbond_it3.383666
X-RAY DIFFRACTIONr_scangle_it5.2914.5655
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 50 -
Rwork0.196 1035 -
obs--92.42 %
Refinement TLS params.Method: refined / Origin x: -4.0849 Å / Origin y: -28.6984 Å / Origin z: -5.2304 Å
111213212223313233
T0.2605 Å20.0895 Å20.0245 Å2-0.1151 Å20.0065 Å2--0.1441 Å2
L0.9659 °2-0.0543 °20.3847 °2-0.6279 °20.4883 °2--4.0157 °2
S-0.0947 Å °-0.0395 Å °0.2065 Å °-0.0746 Å °0.103 Å °-0.0059 Å °-1.006 Å °-0.3126 Å °-0.0083 Å °

+
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