[English] 日本語
Yorodumi
- PDB-5y2s: 7.0 atm CO2-pressurized human carbonic anhydrase II -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5y2s
Title7.0 atm CO2-pressurized human carbonic anhydrase II
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Intermediate states
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 / regulation of intracellular pH / morphogenesis of an epithelium / 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
CARBON DIOXIDE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.9 Å
AuthorsKim, C.U. / Park, S.Y.
Funding support Korea, Republic Of, 3items
OrganizationGrant numberCountry
National Research Foundation of Korea2014R1A2A1A11051254 Korea, Republic Of
National Research Foundation of Korea2016R1A5A1013277 Korea, Republic Of
National Research Foundation of Korea2016R1D1A1A09918187 Korea, Republic Of
CitationJournal: IUCrJ / Year: 2018
Title: Active-site solvent replenishment observed during human carbonic anhydrase II catalysis.
Authors: Kim, J.K. / Lomelino, C.L. / Avvaru, B.S. / Mahon, B.P. / McKenna, R. / Park, S. / Kim, C.U.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5355
Polymers29,2891
Non-polymers2464
Water7,728429
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-40 kcal/mol
Surface area11510 Å2
Unit cell
Length a, b, c (Å)42.305, 41.365, 71.944
Angle α, β, γ (deg.)90.00, 104.12, 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: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 429 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIn chain A, residue number 126 is simply skipped.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 40.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate 100 mM TrisHCl pH 7.8

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 0.9→30 Å / Num. obs: 162430 / % possible obs: 95.2 % / Redundancy: 4.7 % / Net I/σ(I): 14.1
Reflection shellResolution: 0.9→0.92 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.9 / % possible all: 73.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D92

3d92


Resolution: 0.9→28.71 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.339 / SU ML: 0.009 / Cross valid method: THROUGHOUT / ESU R: 0.014 / ESU R Free: 0.015 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.12731 8574 5 %RANDOM
Rwork0.11157 ---
obs0.11236 162430 95.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.536 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 0.9→28.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 13 429 2491
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0192241
X-RAY DIFFRACTIONr_bond_other_d0.0010.022103
X-RAY DIFFRACTIONr_angle_refined_deg2.2231.9553057
X-RAY DIFFRACTIONr_angle_other_deg2.18234892
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8825286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30824.757103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59215379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.204157
X-RAY DIFFRACTIONr_chiral_restr0.1350.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0212559
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02516
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_it2.8330.761081
X-RAY DIFFRACTIONr_mcbond_other2.8550.7581080
X-RAY DIFFRACTIONr_mcangle_it3.8241.1541361
X-RAY DIFFRACTIONr_mcangle_other3.8321.1561362
X-RAY DIFFRACTIONr_scbond_it3.9681.0161160
X-RAY DIFFRACTIONr_scbond_other3.9681.0161160
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9021.411688
X-RAY DIFFRACTIONr_long_range_B_refined8.3329.5523062
X-RAY DIFFRACTIONr_long_range_B_other6.7327.5862723
X-RAY DIFFRACTIONr_rigid_bond_restr7.50934344
X-RAY DIFFRACTIONr_sphericity_free72.298552
X-RAY DIFFRACTIONr_sphericity_bonded14.35554648
LS refinement shellResolution: 0.897→0.921 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 499 -
Rwork0.248 9588 -
obs--76.19 %

+
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