[English] 日本語
Yorodumi
- PDB-5ztp: Carbonic anhydrase from Glaciozyma antarctica -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ztp
TitleCarbonic anhydrase from Glaciozyma antarctica
Componentscarbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / psychrophilic enzyme
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGlaciozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.96 Å
AuthorsJaafar, N.R. / Bakar, A.F.D. / Murad, A.M.A. / Mahadi, N.M. / Jonet, M.A.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilMOSTI_Malaysia Malaysia
CitationJournal: To Be Published
Title: Carbonic anhydrase from Glaciozyma antarctica
Authors: Jaafar, N.R. / Bakar, A.F.D. / Murad, A.M.A. / Mahadi, N.M. / Jonet, M.A.
History
DepositionMay 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 23, 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
B: carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8744
Polymers36,6822
Non-polymers1922
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7380 Å2
ΔGint-89 kcal/mol
Surface area13030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.058, 82.058, 99.280
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein carbonic anhydrase


Mass: 18340.916 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glaciozyma antarctica (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A384E115*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.24 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 20 mM tris hcl, 50 mM NaCl, 10% glycerol, 0.05 mM Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Apr 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.96→40 Å / Num. obs: 8380 / % possible obs: 99.7 % / Redundancy: 6.1 % / Net I/σ(I): 10.7
Reflection shellResolution: 2.96→3.01 Å

-
Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.1data extraction
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LAS

3las


Resolution: 2.96→37.95 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.878 / SU B: 14.78 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.389
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2264 387 4.6 %RANDOM
Rwork0.1788 ---
obs0.181 8370 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 84.51 Å2 / Biso mean: 19.8014 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.15 Å2-0 Å2
2---0.15 Å2-0 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.96→37.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 10 14 2598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192632
X-RAY DIFFRACTIONr_bond_other_d0.0030.022538
X-RAY DIFFRACTIONr_angle_refined_deg1.7391.9673564
X-RAY DIFFRACTIONr_angle_other_deg0.99835840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9455336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.55823.509114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.17115438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.8551518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212968
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02582
LS refinement shellResolution: 2.965→3.041 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 32 -
Rwork0.241 586 -
all-618 -
obs--100 %

+
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