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- PDB-4y0j: H/D exchanged human carbonic anhydrase II pH 6 room temperature n... -

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Basic information

Entry
Database: PDB / ID: 4y0j
TitleH/D exchanged human carbonic anhydrase II pH 6 room temperature neutron crystal structure.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / neutron / proton transfer / H/D exchanged
Function / homology
Function and homology information


positive regulation of dipeptide transmembrane transport / positive regulation of cellular pH reduction / Developmental Lineage of Pancreatic Ductal Cells / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide ...positive regulation of dipeptide transmembrane transport / positive regulation of cellular pH reduction / Developmental Lineage of Pancreatic Ductal Cells / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
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
DEUTERATED WATER / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFisher, S.Z.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer.
Authors: Michalczyk, R. / Unkefer, C.J. / Bacik, J.P. / Schrader, T.E. / Ostermann, A. / Kovalevsky, A.Y. / McKenna, R. / Fisher, S.Z.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 2.0Apr 4, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / diffrn_source ...atom_site / diffrn_source / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _diffrn_source.type / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Nov 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 2.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1362
Polymers29,0711
Non-polymers651
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16910 Å2
ΔGint-17 kcal/mol
Surface area12280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.750, 41.680, 72.950
Angle α, β, γ (deg.)90.00, 104.67, 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: 29070.785 Da / Num. of mol.: 1 / Fragment: UNP residues 3-260
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET / 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: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Large drops 500 microliters in 9-well glass plate in sandwich box set-up. Crystals took 3 months to grow to maximal size.
Temp details: ambient

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: LANSCE / Beamline: PCS / Wavelength: 0.7 - 6.5
DetectorType: 3He-position sensitive detector. / Detector: CCD / Date: Nov 1, 2012
RadiationMonochromator: None / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
10.71
26.51
ReflectionResolution: 2→20 Å / Num. obs: 13799 / % possible obs: 82 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.228 / Net I/σ(I): 4.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 1.5 / % possible all: 70

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Processing

Software
NameClassification
d*TREKdata reduction
CNSrefinement
Cootmodel building
CNSphasing
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1tbt

1tbt


Resolution: 2→20 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.291 --random
Rwork0.263 ---
obs-13799 82 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2494 0 1 139 2634

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