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- PDB-8sd9: Carbonic anhydrase II radiation damage RT 121-150 -

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Basic information

Entry
Database: PDB / ID: 8sd9
TitleCarbonic anhydrase II radiation damage RT 121-150
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / XFEL
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 / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.904 Å
AuthorsCombs, J.E. / Mckenna, R.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2024
Title: XFEL structure of carbonic anhydrase II: a comparative study of XFEL, NMR, X-ray and neutron structures.
Authors: Hull, J.A. / Lee, C. / Kim, J.K. / Lim, S.W. / Park, J. / Park, S. / Lee, S.J. / Park, G. / Eom, I. / Kim, M. / Hyun, H. / Combs, J.E. / Andring, J.T. / Lomelino, C. / Kim, C.U. / McKenna, R.
History
DepositionApr 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release

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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)29,3542
Polymers29,2891
Non-polymers651
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.731, 41.592, 72.769
Angle α, β, γ (deg.)90.00, 104.47, 90.00
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: 29289.062 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 (E. coli) / 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.: 183 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6 M sodium citrate, 50 mM Tris base

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: PAL-XFEL / Beamline: CSI / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 19327 / % possible obs: 98.7 % / Redundancy: 4.3 % / Rrim(I) all: 0.1359 / Net I/σ(I): 13.62
Reflection shellResolution: 1.9→1.93 Å / Num. unique obs: 19327 / Rrim(I) all: 0.1573

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.904→20.451 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 15.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1632 952 4.93 %
Rwork0.136 --
obs0.1373 19317 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.904→20.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 1 183 2243
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092187
X-RAY DIFFRACTIONf_angle_d1.162984
X-RAY DIFFRACTIONf_dihedral_angle_d16.403809
X-RAY DIFFRACTIONf_chiral_restr0.076312
X-RAY DIFFRACTIONf_plane_restr0.01391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9042-2.00450.17621210.15512560X-RAY DIFFRACTION97
2.0045-2.130.17371430.14422651X-RAY DIFFRACTION99
2.13-2.29420.18391520.13912596X-RAY DIFFRACTION100
2.2942-2.52470.18761440.14032643X-RAY DIFFRACTION100
2.5247-2.88920.17911460.14212615X-RAY DIFFRACTION99
2.8892-3.63670.15031280.1332634X-RAY DIFFRACTION98
3.6367-20.450.13491180.12492666X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 11.9138 Å / Origin y: -0.3365 Å / Origin z: 16.1371 Å
111213212223313233
T0.0172 Å2-0.003 Å20 Å2-0.0143 Å20.0029 Å2--0.0133 Å2
L0.1839 °2-0.0502 °20.0051 °2-0.2105 °2-0.0081 °2--0.0819 °2
S-0.0133 Å °-0.0172 Å °0.0085 Å °-0.0337 Å °0.0175 Å °-0.0136 Å °-0.0008 Å °-0.0032 Å °0.031 Å °
Refinement TLS groupSelection details: all

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