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- PDB-5zxw: Crystal structure of human carbonic anhydrase II crystallized by ... -

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Basic information

Entry
Database: PDB / ID: 5zxw
TitleCrystal structure of human carbonic anhydrase II crystallized by ammonium sulfate
ComponentsCarbonic anhydrase 2
KeywordsLYASE / HUMAN CARBONIC ANHYDRASE
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.316 Å
AuthorsKitahara, M. / Fudo, S. / Yoneda, T. / Nukaga, M. / Hoshino, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K08458 Japan
CitationJournal: Cryst.Growth Des. / Year: 2019
Title: Anisotropic Distribution of Ammonium Sulfate Ions in Protein Crystallization
Authors: Kitahara, M. / Fudo, S. / Yoneda, T. / Nukaga, M. / Hoshino, T.
History
DepositionMay 22, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation
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.title / _citation.year
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9763
Polymers29,8151
Non-polymers1612
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-37 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.102, 41.323, 72.130
Angle α, β, γ (deg.)90.000, 104.190, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29814.613 Da / Num. of mol.: 1 / Fragment: UNP residues 5-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET50 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.78 % / Mosaicity: 0.17 °
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.3 / Details: 2.7M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 17, 2016 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.28→41.32 Å / Num. obs: 58025 / % possible obs: 92.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 16.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.038 / Rrim(I) all: 0.072 / Net I/σ(I): 10.4 / Num. measured all: 204824 / Scaling rejects: 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.28-1.33.11.10323450.4360.7261.32776.9
6.99-41.322.80.0443930.9960.030.05394.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation34.97 Å1.76 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.1.27data scaling
MOLREP11.0.05phasing
PHENIX1.13_2998: ???refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EH7

5eh7


Resolution: 1.316→34.965 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 20.61
RfactorNum. reflection% reflection
Rfree0.1982 2669 5 %
Rwork0.1709 --
obs0.1722 53357 93.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.12 Å2 / Biso mean: 20.8256 Å2 / Biso min: 9.08 Å2
Refinement stepCycle: final / Resolution: 1.316→34.965 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2039 0 6 333 2378
Biso mean--43.49 32.93 -
Num. residues----256
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3164-1.34030.37451230.38332323244682
1.3403-1.36610.43021320.34472508264089
1.3661-1.3940.35251310.3312505263690
1.394-1.42430.29341390.27882625276491
1.4243-1.45740.26771360.24872596273291
1.4574-1.49390.2361380.21442620275893
1.4939-1.53430.23351400.20572661280193
1.5343-1.57940.20331410.20032662280394
1.5794-1.63040.19861410.18622685282694
1.6304-1.68870.22551420.17952694283694
1.6887-1.75630.22571410.172679282095
1.7563-1.83620.2131430.16812719286295
1.8362-1.9330.19641430.16542713285695
1.933-2.05410.18911450.15882758290396
2.0541-2.21270.20771440.1572736288096
2.2127-2.43530.171470.15892801294897
2.4353-2.78750.20211460.16762771291797
2.7875-3.51150.18861480.15522817296597
3.5115-34.97750.15331490.14372815296495

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