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- PDB-7u5w: Crystal Structure Analysis of human Carbonic anhydrase 2 -

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Basic information

Entry
Database: PDB / ID: 7u5w
TitleCrystal Structure Analysis of human Carbonic anhydrase 2
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic anhydrase / 19F-Phenylalanine
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 / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / angiotensin-activated signaling pathway / morphogenesis of an epithelium / regulation of intracellular pH / 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, 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.13 Å
AuthorsSeo, H.-S. / Dhe-Paganon, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Crystal Structure Analysis of human Carbonic anhydrase 2
Authors: Seo, H.-S. / Dhe-Paganon, S.
History
DepositionMar 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,5542
Polymers29,4891
Non-polymers651
Water6,449358
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.160, 71.460, 73.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 29488.945 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(DE3) (bacteria) / 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


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 1.89 Å3/Da / Density % sol: 34.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0% PEG1000 and 0.1M Tris pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.13→36.61 Å / Num. obs: 81942 / % possible obs: 97.4 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.52 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.052 / Net I/σ(I): 12.3 / Num. measured all: 276676
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.13-1.151.71565332830.6090.94979.4
3.07-36.633.644.51546242700.0140.02795.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
xia2data scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S73

3s73


Resolution: 1.13→36.61 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.18 4156 5.08 %
Rwork0.1571 77730 -
obs0.1583 81886 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 52.14 Å2 / Biso mean: 17.4522 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: final / Resolution: 1.13→36.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2056 0 1 358 2415
Biso mean--8.42 29.3 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012117
X-RAY DIFFRACTIONf_angle_d1.32882
X-RAY DIFFRACTIONf_dihedral_angle_d9.241283
X-RAY DIFFRACTIONf_chiral_restr0.104299
X-RAY DIFFRACTIONf_plane_restr0.011371
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.13-1.140.34681060.31162015212177
1.14-1.160.30821120.29572263237585
1.16-1.170.26911230.26992349247289
1.17-1.190.28671410.24532437257895
1.19-1.20.27951510.2352561271297
1.2-1.220.22851290.21342567269698
1.22-1.230.21431490.20262629277899
1.23-1.250.2221460.19422610275699
1.25-1.270.21921290.186826472776100
1.27-1.290.21791390.181825852724100
1.29-1.320.1881500.17072650280099
1.32-1.340.20131480.16972581272999
1.34-1.370.19451220.15572668279099
1.37-1.390.17541480.14992610275899
1.39-1.420.21761410.14442621276299
1.42-1.460.16561330.13982652278599
1.46-1.490.18161570.12626132770100
1.49-1.530.17611490.129626292778100
1.53-1.580.15871500.129426622812100
1.58-1.630.15741350.128926732808100
1.63-1.690.16151310.141126502781100
1.69-1.760.15621360.137926692805100
1.76-1.840.17311450.13992631277699
1.84-1.930.16531320.13862655278798
1.93-2.050.15121620.1422602276499
2.05-2.210.17231390.141627002839100
2.21-2.430.16231230.154727032826100
2.43-2.790.19311190.16682724284399
2.79-3.510.19961430.16812655279896
3.51-36.610.15671680.14882719288795

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