[English] 日本語
Yorodumi
- PDB-6lva: Cu- Carbonic Anhydrase II pH 7.8 20 atm CO2 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lva
TitleCu- Carbonic Anhydrase II pH 7.8 20 atm CO2
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / LYASE / metalloenzymes / carbonic anhydrase / enzyme mechanism / metal coordination geometry / proton transfer / biological water dynamics
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 / morphogenesis of an epithelium ...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 / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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
CARBON DIOXIDE / COPPER (II) ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2019R1A2C1004274 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2020
Title: Elucidating the role of metal ions in carbonic anhydrase catalysis.
Authors: Kim, J.K. / Lee, C. / Lim, S.W. / Adhikari, A. / Andring, J.T. / McKenna, R. / Ghim, C.M. / Kim, C.U.
History
DepositionFeb 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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)29,5525
Polymers29,2891
Non-polymers2634
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-19 kcal/mol
Surface area11640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.359, 41.402, 72.307
Angle α, β, γ (deg.)90.000, 103.972, 90.000
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-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 17, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 73862 / % possible obs: 96.9 % / Redundancy: 7.5 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.031 / Rrim(I) all: 0.084 / Net I/σ(I): 25.3
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 3600 / CC1/2: 0.906 / CC star: 0.975 / Rpim(I) all: 0.175 / Rrim(I) all: 0.481 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0124 2015/06/02refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0124phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YUK

5yuk


Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.876 / SU ML: 0.018 / Cross valid method: FREE R-VALUE / ESU R: 0.032 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1419 3775 -
Rwork0.113 --
all0.114 --
obs-73841 96.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 11.628 Å2
Baniso -1Baniso -2Baniso -3
1--0.042 Å2-0 Å2-0.019 Å2
2--0.106 Å20 Å2
3----0.049 Å2
Refinement stepCycle: LAST / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 11 360 2420
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192220
X-RAY DIFFRACTIONr_bond_other_d0.0030.022067
X-RAY DIFFRACTIONr_angle_refined_deg2.461.9523032
X-RAY DIFFRACTIONr_angle_other_deg1.22234805
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.085283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80824.904104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.45215372
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.522157
X-RAY DIFFRACTIONr_chiral_restr0.1830.2317
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0212562
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02513
X-RAY DIFFRACTIONr_nbd_refined0.340.21682
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1970.24018
X-RAY DIFFRACTIONr_nbtor_refined0.1860.22088
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.22076
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2136
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.390.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1470.26
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3260.283
X-RAY DIFFRACTIONr_nbd_other0.2820.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1970.25
X-RAY DIFFRACTIONr_mcbond_it2.4050.7971078
X-RAY DIFFRACTIONr_mcbond_other2.130.7931077
X-RAY DIFFRACTIONr_mcangle_it2.5061.2051361
X-RAY DIFFRACTIONr_mcangle_other2.5191.2071362
X-RAY DIFFRACTIONr_scbond_it3.5451.071142
X-RAY DIFFRACTIONr_scbond_other3.5451.071142
X-RAY DIFFRACTIONr_scangle_it3.9791.491665
X-RAY DIFFRACTIONr_scangle_other3.9781.491666
X-RAY DIFFRACTIONr_lrange_it8.6689.0932858
X-RAY DIFFRACTIONr_lrange_other5.8627.8462653
X-RAY DIFFRACTIONr_sphericity_free46.338588
X-RAY DIFFRACTIONr_sphericity_bonded14.64954488
X-RAY DIFFRACTIONr_rigid_bond_restr6.07934287
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)WRfactor Rwork
1.2-1.2310.2822520.2575002558994.00610.225
1.231-1.2650.2222630.1734936548894.7340.149
1.265-1.3010.1482660.1054753527795.11090.093
1.301-1.3410.1322820.0934654516995.49240.08
1.341-1.3850.1392220.094560499295.79330.078
1.385-1.4340.1432340.0854436485396.22910.075
1.434-1.4880.1212460.0814276468196.60330.073
1.488-1.5480.1222260.0814124449296.83880.074
1.548-1.6170.1232350.0843936429197.20350.079
1.617-1.6960.1261930.0853852415697.32920.081
1.696-1.7870.122080.0883624391297.9550.087
1.787-1.8950.1181800.0913495374498.15710.092
1.895-2.0250.1191670.0943287351298.34850.096
2.025-2.1870.1371600.0993068326798.80620.104
2.187-2.3940.1171490.0982814299598.93150.106
2.394-2.6750.1511280.1092604275399.23720.12
2.675-3.0840.1181040.1152292240899.50170.128
3.084-3.7680.1351320.1231938207899.6150.143
3.768-5.2870.168760.1551524161399.1940.178
5.287-30.0020.271520.27188294598.8360.317

+
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