[English] 日本語
Yorodumi
- PDB-3omx: Crystal structure of Ssu72 with vanadate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3omx
TitleCrystal structure of Ssu72 with vanadate complex
ComponentsCG14216
KeywordsHYDROLASE / transition state / phosphatase / low molecular weight protein tyrosine phosphatase / dephosphorylation / RNA polymerase II / Pta1
Function / homology
Function and homology information


RNA polymerase II transcribes snRNA genes / RNA polymerase II CTD heptapeptide repeat phosphatase activity / mRNA cleavage and polyadenylation specificity factor complex / mRNA 3'-end processing / termination of RNA polymerase II transcription / protein-serine/threonine phosphatase / phosphatase activity / nucleus
Similarity search - Function
Helix Hairpins - #550 / RNA polymerase II subunit A / Ssu72-like protein / Helix Hairpins / Response regulator / Helix non-globular / Special / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
VANADATE ION / RNA polymerase II subunit A C-terminal domain phosphatase SSU72
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3366 Å
AuthorsZhang, Y. / Zhang, M. / Zhang, Y.
CitationJournal: Biochem.J. / Year: 2011
Title: Crystal structure of Ssu72, an essential eukaryotic phosphatase specific for the C-terminal domain of RNA polymerase II, in complex with a transition state analogue.
Authors: Zhang, Y. / Zhang, M. / Zhang, Y.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CG14216
B: CG14216
C: CG14216
D: CG14216
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,3898
Polymers88,9304
Non-polymers4604
Water3,081171
1
A: CG14216
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3472
Polymers22,2321
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CG14216
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3472
Polymers22,2321
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CG14216
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3472
Polymers22,2321
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CG14216
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3472
Polymers22,2321
Non-polymers1151
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)157.616, 102.309, 65.816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein
CG14216 / LD40846p


Mass: 22232.393 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG14216, Dmel_CG14216 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9VWE4
#2: Chemical
ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: VO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.98 Å3/Da / Density % sol: 58.77 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 10% isopropanol, 14-18% PEG4000, VAPOR DIFFUSION, SITTING DROP, temperature 277.0K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.976 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 24, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.3366→48.67 Å / Num. all: 45740 / Num. obs: 45695 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rsym value: 0.07 / Net I/σ(I): 36.5
Reflection shellResolution: 2.3366→2.39 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.761 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3OMW

3omw


Resolution: 2.3366→48.656 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2673 2295 5.04 %random
Rwork0.2046 ---
all0.208 45740 --
obs0.2078 45556 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.002 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--7.6639 Å20 Å20 Å2
2--2.8604 Å2-0 Å2
3---4.8035 Å2
Refinement stepCycle: LAST / Resolution: 2.3366→48.656 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6216 0 20 171 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0326332
X-RAY DIFFRACTIONf_angle_d2.9148516
X-RAY DIFFRACTIONf_dihedral_angle_d22.4242404
X-RAY DIFFRACTIONf_chiral_restr0.201936
X-RAY DIFFRACTIONf_plane_restr0.0121116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3366-2.38740.34571290.27052370X-RAY DIFFRACTION46
2.3874-2.44290.33681370.25322700X-RAY DIFFRACTION52
2.4429-2.5040.3131370.24722666X-RAY DIFFRACTION52
2.504-2.57170.31651370.22682678X-RAY DIFFRACTION52
2.5717-2.64740.27491490.23042701X-RAY DIFFRACTION52
2.6474-2.73280.33211420.22622691X-RAY DIFFRACTION52
2.7328-2.83050.34691430.23722691X-RAY DIFFRACTION52
2.8305-2.94380.35121550.2382679X-RAY DIFFRACTION52
2.9438-3.07780.3071340.21892724X-RAY DIFFRACTION52
3.0778-3.240.29251540.21912699X-RAY DIFFRACTION52
3.24-3.44290.29311600.21242707X-RAY DIFFRACTION53
3.4429-3.70870.26781580.18642724X-RAY DIFFRACTION53
3.7087-4.08170.22491370.19012747X-RAY DIFFRACTION53
4.0817-4.6720.2361210.17042788X-RAY DIFFRACTION53
4.672-5.88460.25711520.18422781X-RAY DIFFRACTION54
5.8846-48.66660.21841500.18472915X-RAY DIFFRACTION56

+
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