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- PDB-6rm1: Human Carbonic Anhydrase II in complex with fragment. -

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Basic information

Entry
Database: PDB / ID: 6rm1
TitleHuman Carbonic Anhydrase II in complex with fragment.
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Inhibitor / Complex / CO2 conversion
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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / 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, 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
3-methylbenzohydrazide / (4-CARBOXYPHENYL)(CHLORO)MERCURY / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsGloeckner, S. / Heine, A. / Klebe, G.
CitationJournal: Biomolecules / Year: 2020
Title: A Proof-of-Concept Fragment Screening of a Hit-Validated 96-Compounds Library against Human Carbonic Anhydrase II.
Authors: Glockner, S. / Heine, A. / Klebe, G.
History
DepositionMay 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4575
Polymers29,8071
Non-polymers6514
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint1 kcal/mol
Surface area11260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.452, 41.466, 71.988
Angle α, β, γ (deg.)90.00, 104.66, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29806.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first 5 amino acids (GSPEF) are remnants of an expression tag.
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pGEX-4T1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Codon Plus / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 170 molecules

#2: Chemical ChemComp-BE7 / (4-CARBOXYPHENYL)(CHLORO)MERCURY / P-CHLOROMERCURIBENZOIC ACID


Mass: 357.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5ClHgO2
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-45L / 3-methylbenzohydrazide


Mass: 150.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: Ammonium sulfate 2.7 M, TRIS 0.1 M, pH = 7.8, saturated with para-Chloromercuribenzoic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2015
RadiationMonochromator: Double Crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.68→41.466 Å / Num. obs: 27053 / % possible obs: 96.8 % / Redundancy: 3.81 % / Biso Wilson estimate: 8.7 Å2 / CC1/2: 0.997 / Rsym value: 0.051 / Net I/σ(I): 19.12
Reflection shellResolution: 1.68→1.78 Å / Redundancy: 3.57 % / Mean I/σ(I) obs: 12.06 / Num. unique obs: 4228 / CC1/2: 0.992 / Rsym value: 0.073 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3KS3

3ks3


Resolution: 1.68→35.629 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 16.42
RfactorNum. reflection% reflectionSelection details
Rfree0.1806 1353 5 %Random selection of 5 %
Rwork0.1528 ---
obs0.1542 27052 96.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.68→35.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 26 166 2203
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082120
X-RAY DIFFRACTIONf_angle_d0.992886
X-RAY DIFFRACTIONf_dihedral_angle_d9.4671235
X-RAY DIFFRACTIONf_chiral_restr0.063302
X-RAY DIFFRACTIONf_plane_restr0.007385
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6797-1.73980.19851300.13792465X-RAY DIFFRACTION94
1.7398-1.80940.19141340.1362544X-RAY DIFFRACTION96
1.8094-1.89180.18311330.14332537X-RAY DIFFRACTION96
1.8918-1.99150.19111330.14342535X-RAY DIFFRACTION97
1.9915-2.11620.19081350.14732558X-RAY DIFFRACTION97
2.1162-2.27960.19441340.15142549X-RAY DIFFRACTION97
2.2796-2.5090.1891360.16322573X-RAY DIFFRACTION97
2.509-2.87190.17891360.16852590X-RAY DIFFRACTION98
2.8719-3.61770.17781390.16582636X-RAY DIFFRACTION98
3.6177-35.63690.15621430.14572712X-RAY DIFFRACTION99

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