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- PDB-6g4t: The crystal structure of uninhibited C183S/C217S mutant of human ... -

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Basic information

Entry
Database: PDB / ID: 6g4t
TitleThe crystal structure of uninhibited C183S/C217S mutant of human CA VII
ComponentsCarbonic anhydrase 7
KeywordsLYASE / Enzyme / catalytic mechanism
Function / homology
Function and homology information


positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding ...positive regulation of cellular pH reduction / regulation of chloride transport / Reversible hydration of carbon dioxide / positive regulation of synaptic transmission, GABAergic / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / neuron cellular homeostasis / one-carbon metabolic process / zinc ion binding / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase VII / 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. ...Carbonic anhydrase VII / 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 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsDi Fiore, A. / D'Ambrosio, K. / De Simone, G.
CitationJournal: Int J Mol Sci / Year: 2018
Title: The Crystal Structure of a hCA VII Variant Provides Insights into the Molecular Determinants Responsible for Its Catalytic Behavior.
Authors: Buonanno, M. / Di Fiore, A. / Langella, E. / D'Ambrosio, K. / Supuran, C.T. / Monti, S.M. / De Simone, G.
History
DepositionMar 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9912
Polymers30,9261
Non-polymers651
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-38 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.300, 89.380, 44.370
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Carbonic anhydrase 7 / / Carbonate dehydratase VII / Carbonic anhydrase VII / CA-VII


Mass: 30925.693 Da / Num. of mol.: 1 / Mutation: C183S, C217S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA7 / Production host: Escherichia coli (E. coli) / References: UniProt: P43166, 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 / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 25% (w/v) polyethylene glycol 3350, 0.1 M Tris, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jan 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.91→31.5 Å / Num. obs: 20846 / % possible obs: 98.8 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 14.7
Reflection shellResolution: 1.91→1.94 Å / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 2.03 / % possible all: 87.3

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Processing

Software
NameVersionClassification
CNSrefinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ML5

3ml5


Resolution: 1.91→31.49 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2441 959 4.5 %
Rwork0.1964 --
obs-19750 93.5 %
Solvent computationBsol: 37.9033 Å2
Displacement parametersBiso max: 56.27 Å2 / Biso mean: 21.0916 Å2 / Biso min: 7.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.051 Å2-0 Å2-0 Å2
2--3.89 Å2-0 Å2
3---0.161 Å2
Refinement stepCycle: final / Resolution: 1.91→31.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2055 0 1 162 2218
Biso mean--13.79 25.63 -
Num. residues----259
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_d1.423
X-RAY DIFFRACTIONc_mcbond_it1.3961.5
X-RAY DIFFRACTIONc_scbond_it1.9812
X-RAY DIFFRACTIONc_mcangle_it2.2092
X-RAY DIFFRACTIONc_scangle_it2.882.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.91-1.980.3442770.25861478155575.5
1.98-2.060.3234840.30361713179786.5
2.06-2.150.28271060.22621790189691.3
2.15-2.260.286910.19511858194993.7
2.26-2.410.28541080.211854196294.2
2.41-2.590.268850.19761949203496.7
2.59-2.850.25791100.191964207498.2
2.85-3.270.1999960.18611990208699.1
3.27-4.110.2079910.18022058214999.7
4.11-31.490.20791110.172137224899.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4ion_patch.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param

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