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- PDB-5ztp: Carbonic anhydrase from Glaciozyma antarctica -

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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
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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

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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
Has protein modificationN

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Experimental details

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Experiment

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

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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

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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

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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 %

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