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- PDB-1lzv: Site-Specific Mutant (Tyr7 replaced with His) of Human Carbonic A... -

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Basic information

Entry
Database: PDB / ID: 1lzv
TitleSite-Specific Mutant (Tyr7 replaced with His) of Human Carbonic Anhydrase II
ComponentsCarbonic Anhydrase II
KeywordsLYASE / Twisted Beta Sheet / Zinc Metalloenzyme
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 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTu, C.K. / Qian, M. / An, H. / Wadhwa, N.R. / Duda, D.M. / Yoshioka, C. / Pathak, Y. / McKenna, R. / Laipis, P.J. / Silverman, D.N.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Kinetic analysis of multiple proton shuttles in the active site of human carbonic anhydrase.
Authors: Tu, C. / Qian, M. / An, H. / Wadhwa, N.R. / Duda, D. / Yoshioka, C. / Pathak, Y. / McKenna, R. / Laipis, P.J. / Silverman, D.N.
History
DepositionJun 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE Residue 125 is covalently bound to 127. Number 126 is not used as a matter of convention ...SEQUENCE Residue 125 is covalently bound to 127. Number 126 is not used as a matter of convention for sequence alignments.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic Anhydrase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3292
Polymers29,2641
Non-polymers651
Water1,00956
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.871, 41.585, 72.951
Angle α, β, γ (deg.)90.00, 104.75, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe Biological Assembly is a Monomer Constructed from Chain A

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Components

#1: Protein Carbonic Anhydrase II / Carbonate dehydratase II / CA-II


Mass: 29264.035 Da / Num. of mol.: 1 / Mutation: Y7H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium Sulfate, Tris HCL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 40 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
250 mMTris-HCl1droppH7.8
32.4-2.65 Mammonium sulfate1reservoir
450 mMTris-HCl1reservoirpH7.8

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.548 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 10, 2002
RadiationMonochromator: Osmic Optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.548 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 11305 / % possible obs: 85 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.151
Reflection shellResolution: 2.3→2.38 Å / % possible all: 85
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 9586 / Rmerge(I) obs: 0.151
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 87.3 % / Num. unique obs: 979 / Rmerge(I) obs: 0.401

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G0F

1g0f


Resolution: 2.3→19.94 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 481 5.4 %RANDOM
Rwork0.186 ---
all-9586 --
obs-8989 80.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.3849 Å2 / ksol: 0.342336 e/Å3
Displacement parametersBiso mean: 23.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å22.12 Å2
2---3.85 Å20 Å2
3---3.59 Å2
Refine analyzeLuzzati coordinate error free: 0.32 Å / Luzzati sigma a free: 0.35 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2036 0 1 56 2093
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.6
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.812.5
LS refinement shellResolution: 2.3→2.38 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.401 0 -
obs-979 87.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.366
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
LS refinement shell
*PLUS
Rfactor Rwork: 0.401

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