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- PDB-7u5x: Crystal Structure Analysis of human Carbonic anhydrase 2 -

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Basic information

Entry
Database: PDB / ID: 7u5x
TitleCrystal Structure Analysis of human Carbonic anhydrase 2
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Carbonic anhydrase / 19F-Tyrosine
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 / 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 / zinc ion binding / extracellular exosome / plasma membrane / cytoplasm / cytosol
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: 1.04 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)29,4822
Polymers29,4171
Non-polymers651
Water6,395355
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)42.230, 41.260, 72.070
Angle α, β, γ (deg.)90.000, 104.170, 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: 29416.980 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.: 355 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2.4 M Sodium malate, 100mM Tris pH 8.8

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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: Sep 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.04→69.88 Å / Num. obs: 90335 / % possible obs: 78.2 % / Redundancy: 6.2 % / Biso Wilson estimate: 13 Å2 / Rpim(I) all: 0.026 / Rrim(I) all: 0.067 / Net I/σ(I): 13.7 / Num. measured all: 564544
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) all% possible all
1.04-1.062.90.712654420.8361.4947.6
2.82-70.046.429.43762759120.020.05399.4

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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: 1.04→69.88 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1705 4440 4.92 %
Rwork0.147 85873 -
obs0.1482 90313 78.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 51.2 Å2 / Biso mean: 19.106 Å2 / Biso min: 9.29 Å2
Refinement stepCycle: final / Resolution: 1.04→69.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 1 355 2408
Biso mean--10.8 30.75 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012229
X-RAY DIFFRACTIONf_angle_d1.4453054
X-RAY DIFFRACTIONf_dihedral_angle_d9.481296
X-RAY DIFFRACTIONf_chiral_restr0.112309
X-RAY DIFFRACTIONf_plane_restr0.011398
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 (%)
1.04-1.050.353100.37952062166
1.05-1.060.3803250.357844947412
1.06-1.080.3517320.271570273419
1.08-1.090.2193520.2668969102127
1.09-1.110.2634480.23861206125433
1.11-1.120.2342750.21961451152640
1.12-1.140.2212920.19991759185148
1.14-1.150.2392790.17852078215757
1.15-1.170.18551010.17212400250165
1.17-1.190.19651480.16722631277973
1.19-1.210.20211620.16253117327985
1.21-1.230.19531900.15723510370097
1.23-1.260.18881820.16023638382099
1.26-1.280.16471900.15753626381699
1.28-1.310.17341600.14113623378399
1.31-1.340.17321570.13443639379699
1.34-1.370.15552060.13323602380898
1.37-1.410.17141870.13163565375298
1.41-1.450.16021960.13133466366296
1.45-1.50.16341930.12863609380299
1.5-1.550.16882160.1336343850100
1.55-1.620.16151980.137736363834100
1.62-1.690.18131820.13833682386499
1.69-1.780.16061880.13673622381099
1.78-1.890.15641840.13773632381699
1.89-2.040.15582010.13633589379098
2.04-2.240.15572210.138636603881100
2.24-2.570.1771880.150737093897100
2.57-3.230.1941800.16183684386499
3.23-69.880.1621970.14843779397699

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