[English] 日本語
Yorodumi
- PDB-4oq2: 5hmC specific restriction endonuclease PvuRTs1I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4oq2
Title5hmC specific restriction endonuclease PvuRTs1I
ComponentsRestriction endonuclease PvuRts1 I
KeywordsHYDROLASE / cytosine hydroxymethylation / PD-(D/E)XK nuclease domain / SRA DNA binding domain / restriction endonuclease / 5-hydroxymethylcytosine / DNA
Function / homologySET and RING associated domain / : / SET and RING associated domain / Restriction endonuclease PvuRts1 I-like, N-terminal / endonuclease activity / Restriction endonuclease PvuRts1 I
Function and homology information
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsKazrani, A.A. / Kowalska, M. / Czapinska, H. / Bochtler, M.
CitationJournal: Nucleic Acids Res. / Year: 2014
Title: Crystal structure of the 5hmC specific endonuclease PvuRts1I.
Authors: Kazrani, A.A. / Kowalska, M. / Czapinska, H. / Bochtler, M.
History
DepositionFeb 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2014Group: Database references
Revision 1.2Jun 4, 2014Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Restriction endonuclease PvuRts1 I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1032
Polymers35,8651
Non-polymers2381
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.990, 61.990, 210.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsTHE WILD-TYPE PROTEIN IS A DIMER. THE N-TERMINAL HISTIDINE TAG MAY FAVOR THE MONOMERIC FORM FOUND IN OUR CRYSTALS.

-
Components

#1: Protein Restriction endonuclease PvuRts1 I / Restriction endonuclease PvuRts1I / PvuRtsI1 restriction endonuclease


Mass: 35864.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus vulgaris (bacteria) / Gene: 1239102, pvuRts1I / Plasmid: pET15bMOD / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q52612, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.47 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% w/v PEG4000, 20% v/v glycerol, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine, 0.1 M MOPS/HEPES sodium, pH 7.5, for ...Details: 10% w/v PEG4000, 20% v/v glycerol, 20 mM D-glucose, 20 mM D-mannose, 20 mM D-galactose, 20 mM L-fucose, 20 mM D-xylose, 20 mM N-acetyl-D-glucosamine, 0.1 M MOPS/HEPES sodium, pH 7.5, for cryoprotection, crystals were transferred to a variant of the buffer with 28% v/v glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. all: 17509 / Num. obs: 17509 / % possible obs: 96.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 19.5
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1275 / Rsym value: 0.97 / % possible all: 99

-
Processing

Software
NameVersionClassification
SHELXDEphasing
DMmodel building
PHENIXmodel building
REFMAC5.5.0066refinement
XDSdata reduction
XSCALEdata scaling
DMphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.35→43.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.935 / SU B: 18.331 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED. THE LOOP FOLLOWING THE ACTIVE SITE (RESIDUES 70-76) HAS BEEN MODELED TENTATIVELY BUT IT IS MOST LIKELY ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TLS REFINEMENT HAS BEEN USED. THE LOOP FOLLOWING THE ACTIVE SITE (RESIDUES 70-76) HAS BEEN MODELED TENTATIVELY BUT IT IS MOST LIKELY DISORDERED DUE TO THE ABSENCE OF CATALYTIC METAL IONS AND/OR TARGET DNA.
RfactorNum. reflection% reflectionSelection details
Rfree0.25397 897 5.1 %RANDOM
Rwork0.20305 ---
all0.20563 17495 --
obs0.20563 17495 96.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.387 Å2
Baniso -1Baniso -2Baniso -3
1-0.85 Å20 Å20 Å2
2--0.85 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.35→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 15 55 2539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0212579
X-RAY DIFFRACTIONr_bond_other_d00.022272
X-RAY DIFFRACTIONr_angle_refined_deg1.2931.9263488
X-RAY DIFFRACTIONr_angle_other_deg0.6435260
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8515302
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.51522.945146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.29915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5921526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2358
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022899
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02589
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_it0.5771.51493
X-RAY DIFFRACTIONr_mcbond_other0.0951.5611
X-RAY DIFFRACTIONr_mcangle_it1.10822407
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.64631086
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7654.51081
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 50 -
Rwork0.306 1218 -
obs-1268 98.83 %
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)
12.07880.3605-0.22681.8216-1.78173.63310.09590.3245-0.212-0.06090.14370.03890.2301-0.5251-0.23950.34140.05470.03820.55220.04760.064226.80419.43261.163
22.8760.0842-0.60511.3136-0.43592.29980.0119-0.0068-0.29930.1098-0.0051-0.07340.0582-0.072-0.00670.3014-0.0151-0.04690.34560.03870.04628.9326.2684.603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 141
2X-RAY DIFFRACTION2A142 - 290

+
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