[English] 日本語
Yorodumi
- PDB-9gaj: X-ray structure of HCA(II)/aromatic foldamer complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gaj
TitleX-ray structure of HCA(II)/aromatic foldamer complex
Components
  • Aromatic foldamer
  • Carbonic anhydrase 2
KeywordsPROTEIN BINDING / arbonic anhydrase / aromatic oligoamide foldamer
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 activity / cyanamide hydratase / 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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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 / 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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsWang, L. / Langlois d'Estaintot, B. / Fischer, L. / Huc, I.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: X-ray structure of HCA(II)/aromatic foldamer complex
Authors: Wang, L. / Langlois d'Estaintot, B. / Fischer, L. / Huc, I.
History
DepositionJul 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 6, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Aromatic foldamer
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6024
Polymers32,4442
Non-polymers1582
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology, Homology of the HCA2/foldamer complex with 6Q9T, surface plasmon resonance, Nanomolar affinity has been measured for this complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.512, 81.515, 45.893
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
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 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P00918, carbonic anhydrase
#2: Protein/peptide Aromatic foldamer


Mass: 3155.203 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.45 % / Description: Platelet
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: lithium sulfate, TRIS, PEG 4000, sodium azide

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2020
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.64→45.893 Å / Num. obs: 67930 / % possible obs: 97 % / Redundancy: 2.43 % / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.056 / Rrim(I) all: 0.092 / Net I/σ(I): 7.34
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
1.64-1.742.310.51107920.229195.7
1.74-1.862.451.02103540.48197.3
1.86-22.532.1297950.789198.8
2-2.22.493.8290210.923198.7
2.2-2.452.326.0280010.966197.2
2.45-2.832.4710.3270930.986197.5
2.83-3.472.518.759090.996196.3
3.47-4.892.3226.344540.997193.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
pointlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTv4.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→40.76 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.261 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21085 1131 3.1 %RANDOM
Rwork0.18359 ---
obs0.18448 35448 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.218 Å2
Baniso -1Baniso -2Baniso -3
1-1.01 Å2-0 Å20 Å2
2---2.05 Å2-0 Å2
3---1.05 Å2
Refinement stepCycle: 1 / Resolution: 1.64→40.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2295 0 7 278 2580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122389
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162128
X-RAY DIFFRACTIONr_angle_refined_deg1.0251.7853240
X-RAY DIFFRACTIONr_angle_other_deg0.3931.864896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1195262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.87457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46410353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2305
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023260
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02577
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_it2.0082.0731057
X-RAY DIFFRACTIONr_mcbond_other2.0052.0721056
X-RAY DIFFRACTIONr_mcangle_it3.0993.691302
X-RAY DIFFRACTIONr_mcangle_other3.13.6891299
X-RAY DIFFRACTIONr_scbond_it2.7562.4871332
X-RAY DIFFRACTIONr_scbond_other2.7552.491333
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3454.3851937
X-RAY DIFFRACTIONr_long_range_B_refined7.25726.852791
X-RAY DIFFRACTIONr_long_range_B_other7.25626.862792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.64→1.68 Å
RfactorNum. reflection% reflection
Rfree0.385 78 -
Rwork0.412 2455 -
obs--95.77 %
Refinement TLS params.Method: refined / Origin x: 21.1514 Å / Origin y: 12.4762 Å / Origin z: 11.3609 Å
111213212223313233
T0.1511 Å20.0141 Å20.0059 Å2-0.1268 Å20.0004 Å2--0.0033 Å2
L0.7612 °2-0.3227 °2-0.3125 °2-1.588 °20.4667 °2--0.7546 °2
S0.0842 Å °0.049 Å °0.0399 Å °-0.2787 Å °-0.0406 Å °-0.0297 Å °-0.049 Å °-0.0058 Å °-0.0436 Å °

+
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