[English] 日本語
Yorodumi
- PDB-4zao: Genetically engineered Carbonic anhydrase IX -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4zao
TitleGenetically engineered Carbonic anhydrase IX
ComponentsCarbonic anhydrase 2
KeywordsLYASE / CA IX mimic
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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsPinard, M.A. / Aggarwal, M.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: A sucrose-binding site provides a lead towards an isoform-specific inhibitor of the cancer-associated enzyme carbonic anhydrase IX.
Authors: Pinard, M.A. / Aggarwal, M. / Mahon, B.P. / Tu, C. / McKenna, R.
History
DepositionApr 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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)29,2662
Polymers29,2011
Non-polymers651
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area11610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.787, 41.231, 72.044
Angle α, β, γ (deg.)90.00, 103.83, 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 / Carbonic ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Carbonic anhydrase IX mimic


Mass: 29200.887 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 / Water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.8 / Details: 10 mg/ml in 50 mM Tris-HCl at ph 7.8 / PH range: 7.0-9.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.918 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 21707 / % possible obs: 97.5 % / Redundancy: 2.7 % / Net I/σ(I): 4559
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 2.4 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
PHENIXDEV_1839refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.8→19.88 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.97 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2048 1092 5.03 %
Rwork0.175 --
obs0.1766 21693 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 1 169 2212
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062203
X-RAY DIFFRACTIONf_angle_d1.0443004
X-RAY DIFFRACTIONf_dihedral_angle_d13.457818
X-RAY DIFFRACTIONf_chiral_restr0.045312
X-RAY DIFFRACTIONf_plane_restr0.005396
LS refinement shellResolution: 1.8006→1.8825 Å
RfactorNum. reflection% reflection
Rfree0.2227 134 -
Rwork0.1639 2512 -
obs--95 %
Refinement TLS params.Method: refined / Origin x: 11.7188 Å / Origin y: -1.5512 Å / Origin z: 16.3058 Å
111213212223313233
T0.0463 Å20.0015 Å20.0038 Å2-0.04 Å20.0014 Å2--0.0491 Å2
L0.7363 °2-0.0628 °20.1608 °2-0.4333 °2-0.0378 °2--0.5605 °2
S-0.0065 Å °-0.01 Å °0.0619 Å °-0.0093 Å °0.0042 Å °0.0181 Å °-0.0078 Å °0.02 Å °-0.0001 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