[English] 日本語
Yorodumi
- PDB-5h4h: Structure of PIN-domain protein (VapC4 toxin) from Pyrococcus hor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5h4h
TitleStructure of PIN-domain protein (VapC4 toxin) from Pyrococcus horikoshii determined at 2.2 A resolution
ComponentsRibonuclease VapC4
KeywordsHYDROLASE / Pyrococcus horikoshii / hypothetical protein / PIN-domain
Function / homology
Function and homology information


RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Probable ribonuclease VapC, Thermococci / : / VapC family / 5'-nuclease / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Ribonuclease VapC4
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.23 Å
AuthorsBiswas, A. / Hatti, K. / Srinivasan, N. / Murthy, M.R.N. / Sekar, K.
CitationJournal: J. Struct. Biol. / Year: 2017
Title: Structure determination of contaminant proteins using the MarathonMR procedure
Authors: Hatti, K. / Biswas, A. / Chaudhary, S. / Dadireddy, V. / Sekar, K. / Srinivasan, N. / Murthy, M.R.N.
History
DepositionOct 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 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: Ribonuclease VapC4
B: Ribonuclease VapC4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6454
Polymers34,4212
Non-polymers2252
Water34219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-32 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.970, 45.260, 53.620
Angle α, β, γ (deg.)90.00, 104.75, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Ribonuclease VapC4 / PIN-domain protein


Mass: 17210.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Strain: OT3 / Gene: vapC4, PH0500 / Production host: Escherichia coli (E. coli)
References: UniProt: O58236, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 1.77 Å3/Da / Density % sol: 30.58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Sodium acetate trihydrate, 0.1M Tris-HCl, 30%(w/v) PEG 4000

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.54179 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.21→51.85 Å / Num. obs: 11886 / % possible obs: 97.2 % / Redundancy: 3.3 % / Net I/σ(I): 8.5
Reflection shellResolution: 2.21→2.29 Å / Redundancy: 3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.54 / % possible all: 71.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V96

1v96


Resolution: 2.23→51.85 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 9.757 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 0.514 / ESU R Free: 0.268 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25904 661 5.6 %RANDOM
Rwork0.20707 ---
obs0.21012 11212 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å2-0.76 Å2
2--0.94 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: 1 / Resolution: 2.23→51.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2285 0 2 19 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.022332
X-RAY DIFFRACTIONr_bond_other_d0.0010.022341
X-RAY DIFFRACTIONr_angle_refined_deg1.2361.9993174
X-RAY DIFFRACTIONr_angle_other_deg0.90935394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6155291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50225.38591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77315435
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.927159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212524
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02453
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_it1.0442.781158
X-RAY DIFFRACTIONr_mcbond_other1.0412.7781157
X-RAY DIFFRACTIONr_mcangle_it1.7774.161445
X-RAY DIFFRACTIONr_mcangle_other1.7764.1621446
X-RAY DIFFRACTIONr_scbond_it1.1342.9361174
X-RAY DIFFRACTIONr_scbond_other1.1332.9381175
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9424.3351728
X-RAY DIFFRACTIONr_long_range_B_refined3.0933.0962590
X-RAY DIFFRACTIONr_long_range_B_other3.08833.1082590
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.232→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 41 -
Rwork0.259 797 -
obs--97.33 %

+
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