[English] 日本語
Yorodumi
- PDB-8sd6: Carbonic anhydrase II radiation damage RT 31-60 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8sd6
TitleCarbonic anhydrase II radiation damage RT 31-60
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / XFEL
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.397 Å
AuthorsCombs, J.E. / Mckenna, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures.
Authors: Hull, J.A. / Lee, C. / Kim, J.K. / Lim, S.W. / Park, J. / Park, S. / Lee, S.J. / Park, G. / Eom, I. / Kim, M. / Hyun, H. / Combs, J.E. / Andring, J.T. / Lomelino, C. / Kim, C.U. / McKenna, R.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3542
Polymers29,2891
Non-polymers651
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.574, 41.327, 72.363
Angle α, β, γ (deg.)90.00, 104.28, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris base

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: CSI / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.397→30 Å / Num. obs: 48076 / % possible obs: 99.2 % / Redundancy: 5.7 % / Rrim(I) all: 0.1374 / Net I/σ(I): 16.05
Reflection shellResolution: 1.397→1.42 Å / Num. unique obs: 48076 / Rrim(I) all: 0.2175

-
Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.397→24.653 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 14.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1536 2410 5.02 %
Rwork0.1374 --
obs0.1382 48055 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.397→24.653 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 1 177 2237
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082187
X-RAY DIFFRACTIONf_angle_d1.0582984
X-RAY DIFFRACTIONf_dihedral_angle_d16.3809
X-RAY DIFFRACTIONf_chiral_restr0.097312
X-RAY DIFFRACTIONf_plane_restr0.008391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3971-1.42560.26021550.22222536X-RAY DIFFRACTION93
1.4256-1.45660.19311430.20912619X-RAY DIFFRACTION99
1.4566-1.49050.21361340.19172707X-RAY DIFFRACTION99
1.4905-1.52780.17871520.17652668X-RAY DIFFRACTION99
1.5278-1.56910.18561540.17172643X-RAY DIFFRACTION99
1.5691-1.61520.18851270.16542672X-RAY DIFFRACTION99
1.6152-1.66730.21231260.16012687X-RAY DIFFRACTION99
1.6673-1.72690.18051400.15362711X-RAY DIFFRACTION99
1.7269-1.7960.16581610.1492678X-RAY DIFFRACTION99
1.796-1.87780.15661520.14122663X-RAY DIFFRACTION100
1.8778-1.97670.14581300.13942719X-RAY DIFFRACTION100
1.9767-2.10050.14051340.13022687X-RAY DIFFRACTION100
2.1005-2.26260.14311500.13442719X-RAY DIFFRACTION100
2.2626-2.49010.16961400.13472709X-RAY DIFFRACTION100
2.4901-2.84990.16211520.1422705X-RAY DIFFRACTION100
2.8499-3.58880.15431180.13712768X-RAY DIFFRACTION100
3.5888-24.650.12471420.11662754X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 11.8152 Å / Origin y: -0.3124 Å / Origin z: 15.9863 Å
111213212223313233
T0.1429 Å2-0.0068 Å20.001 Å2-0.1427 Å20.0031 Å2--0.1464 Å2
L0.8061 °2-0.133 °2-0.0033 °2-0.8184 °20.0578 °2--0.8216 °2
S-0.0138 Å °-0.0195 Å °0.0126 Å °-0.0435 Å °0.0174 Å °-0.0205 Å °0.0072 Å °0.0197 Å °0 Å °
Refinement TLS groupSelection details: all

+
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