[English] 日本語
Yorodumi
- PDB-6b00: Thermostabilized mutant of human carbonic anhydrase II - A65T L10... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b00
TitleThermostabilized mutant of human carbonic anhydrase II - A65T L100H K154N L224S L240P A248T
ComponentsCarbonic anhydrase 2
KeywordsLYASE / carbon sequestration / thermostable / protein engineering
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 / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 II / Alpha carbonic anhydrase / 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 ...Carbonic Anhydrase II / Alpha carbonic anhydrase / 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 / Roll / Alpha Beta
Similarity search - Domain/homology
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsKean, K.M. / Karplus, P.A.
CitationJournal: Protein Sci. / Year: 2018
Title: Structural insights into a thermostable variant of human carbonic anhydrase II.
Authors: Kean, K.M. / Porter, J.J. / Mehl, R.A. / Karplus, P.A.
History
DepositionSep 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_radiation_wavelength.wavelength

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2873
Polymers30,1301
Non-polymers1582
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area420 Å2
ΔGint-40 kcal/mol
Surface area11750 Å2
Unit cell
Length a, b, c (Å)47.620, 43.760, 57.990
Angle α, β, γ (deg.)90.00, 100.72, 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: 30129.773 Da / Num. of mol.: 1 / Mutation: A65T, L100H, K153N, L223S, L239P, A247T
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 5

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.9737.42
21.9737.42
31.9737.42
41.9737.42
51.9737.42
Crystal grow
Temperature (K)Crystal-IDMethodDetails
2781vapor diffusion, hanging drop50 mM Tris pH 8, 2.5 M ammonium sulfate
2782vapor diffusion, hanging drop50 mM Tris pH 8, 2.5 M ammonium sulfate
2783vapor diffusion, hanging drop50 mM Tris pH 8, 2.5 M ammonium sulfate
2784vapor diffusion, hanging drop50 mM Tris pH 8, 2.5 M ammonium sulfate
2785vapor diffusion, hanging drop50 mM Tris pH 8, 2.5 M ammonium sulfate

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
31003
41004
51005
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211
SYNCHROTRONALS 5.0.220.886
SYNCHROTRONALS 5.0.230.886
SYNCHROTRONALS 5.0.240.886
SYNCHROTRONALS 5.0.250.886
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDFeb 8, 2015
ADSC QUANTUM 315r2CCDSep 4, 2015
ADSC QUANTUM 315r3CCDSep 4, 2015
ADSC QUANTUM 315r4CCDSep 5, 2015
ADSC QUANTUM 315r5CCDSep 4, 2015
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
3SINGLE WAVELENGTHMx-ray3
4SINGLE WAVELENGTHMx-ray4
5SINGLE WAVELENGTHMx-ray5
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.8861
31
41
51
Reflection

Entry-ID: 6B00

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)CC1/2Rrim(I) allDiffraction-IDNet I/σ(I)
1.11-46.737440280.16.120.990.053120.22
0.9-23.515886690.93.30.990.04427.32
0.9-23.1755679032.81.220.990.04739.38
0.9-18.1513447920.11.40.990.1546.57
0.9-23.21213913080.11.260.990.04557.63

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1CA2

1ca2


Resolution: 0.9→46.788 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1442 8058 4.99 %random selection
Rwork0.1196 ---
obs0.1208 161593 93.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 0.9→46.788 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2102 0 7 409 2518
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142480
X-RAY DIFFRACTIONf_angle_d1.343419
X-RAY DIFFRACTIONf_dihedral_angle_d12.576950
X-RAY DIFFRACTIONf_chiral_restr0.109352
X-RAY DIFFRACTIONf_plane_restr0.011458
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.9-0.91960.45493710.43897503X-RAY DIFFRACTION73
0.9196-0.9410.39124220.39638067X-RAY DIFFRACTION79
0.941-0.96450.35834460.3478525X-RAY DIFFRACTION83
0.9645-0.99060.31854530.30188766X-RAY DIFFRACTION86
0.9906-1.01970.26124840.2579077X-RAY DIFFRACTION89
1.0197-1.05270.23915160.2069381X-RAY DIFFRACTION92
1.0527-1.09030.18935040.1749773X-RAY DIFFRACTION95
1.0903-1.13390.18395270.150810107X-RAY DIFFRACTION98
1.1339-1.18550.14025600.114910134X-RAY DIFFRACTION99
1.1855-1.24810.13155250.104110240X-RAY DIFFRACTION100
1.2481-1.32630.12935360.09710275X-RAY DIFFRACTION100
1.3263-1.42870.12665440.095510242X-RAY DIFFRACTION100
1.4287-1.57240.1195420.091110326X-RAY DIFFRACTION100
1.5724-1.80.10985190.087710335X-RAY DIFFRACTION100
1.8-2.26780.10775420.085810375X-RAY DIFFRACTION100
2.2678-46.85180.12895670.10210409X-RAY DIFFRACTION99

+
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