[English] 日本語
Yorodumi
- PDB-6x2d: Crystal Structure of DNase I Domain of Ribonuclease E from Vibrio... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6x2d
TitleCrystal Structure of DNase I Domain of Ribonuclease E from Vibrio cholerae
ComponentsRibonuclease E
KeywordsRNA BINDING PROTEIN / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding ...ribonuclease E / ribonuclease E activity / tRNA processing / mRNA catabolic process / RNA nuclease activity / RNA processing / RNA endonuclease activity / cytoplasmic side of plasma membrane / rRNA processing / tRNA binding / rRNA binding / magnesium ion binding / zinc ion binding / cytoplasm
Similarity search - Function
Ribonuclease E/G / RNA-binding protein AU-1/Ribonuclease E/G / Ribonuclease E / Ribonuclease E/G family / RNA-binding domain, S1 / S1 domain profile. / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
IODIDE ION / Ribonuclease E
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMinasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of DNase I Domain of Ribonuclease E from Vibrio cholerae.
Authors: Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Wiersum, G. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionMay 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease E
B: Ribonuclease E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8379
Polymers25,9492
Non-polymers8887
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-13 kcal/mol
Surface area12100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.614, 58.812, 47.046
Angle α, β, γ (deg.)90.000, 108.160, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribonuclease E / / RNase E


Mass: 12974.358 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: rne, VC_2030 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): (DE3)magic / References: UniProt: Q9KQG8, ribonuclease E
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Protein: 7.9 mg/ml, 0.01M Tris pH 8.3; Screen: PACT (F3), 0.2M Sodium iodide, 0.1M Bis-Tris propane pH 6.5, 20% (w/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 17, 2020 / Details: Be
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 17863 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 34.1 Å2 / CC1/2: 0.985 / CC star: 0.996 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.041 / Rrim(I) all: 0.097 / Rsym value: 0.088 / Χ2: 1.466 / Net I/σ(I): 21.9
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6 % / Rmerge(I) obs: 0.759 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 897 / CC1/2: 0.927 / CC star: 0.981 / Rpim(I) all: 0.339 / Rrim(I) all: 0.833 / Rsym value: 0.759 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vrt

2vrt


Resolution: 1.85→29.41 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.97 / SU ML: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 887 5 %RANDOM
Rwork0.2067 ---
obs0.2085 16959 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 103.88 Å2 / Biso mean: 43.735 Å2 / Biso min: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å21.64 Å2
2---1.57 Å20 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 1.85→29.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 9 75 1793
Biso mean--80.56 48.64 -
Num. residues----217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0131736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171716
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.6522336
X-RAY DIFFRACTIONr_angle_other_deg0.411.5853933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0495217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.20419.28125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.08415318
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4341532
X-RAY DIFFRACTIONr_chiral_restr0.0570.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.050.021977
X-RAY DIFFRACTIONr_gen_planes_other0.0440.02395
LS refinement shellResolution: 1.852→1.9 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 67 -
Rwork0.249 1168 -
all-1235 -
obs--93.84 %
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)
13.7316-0.0183-2.2391.1708-0.47271.6657-0.1995-0.11530.06-0.03370.0769-0.12480.32780.03890.12260.31410.00450.1650.0082-0.00950.10383.543-1.871-3.557
21.60880.1813-0.88840.99460.39931.5445-0.05860.0853-0.0696-0.0947-0.0033-0.15950.0411-0.06750.06190.23660.00540.11670.03270.00090.07882.0756.76-6.358
32.45060.47021.34960.10180.05125.116-0.03710.09580.0638-0.01420.03150.0034-0.0247-0.18420.00560.21650.00890.08870.07370.00380.0759-5.97510.595-6.351
41.8539-1.854-1.15012.17571.9452.7566-0.15770.1976-0.29120.3887-0.21280.32850.7945-0.20060.37050.3859-0.08820.21320.0444-0.07430.1814-16.032-1.32713.141
51.7194-2.0084-1.01262.78940.21782.8222-0.20510.0359-0.15440.22980.03940.19840.1926-0.11690.16570.1885-0.01680.12050.06760.0460.1439-14.258.3916.7
61.1362-1.58630.33072.2294-0.64174.0944-0.1252-0.0865-0.01510.19050.12650.03650.11440.2925-0.00120.20510.02710.10010.11560.01780.0608-3.9678.53217.06
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 317
2X-RAY DIFFRACTION2A318 - 361
3X-RAY DIFFRACTION3A362 - 390
4X-RAY DIFFRACTION4B279 - 312
5X-RAY DIFFRACTION5B313 - 361
6X-RAY DIFFRACTION6B362 - 390

+
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