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- PDB-4hf3: Activity Enhancers of H64A Variant of Human Carbonic Anhydrase II... -

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Basic information

Entry
Database: PDB / ID: 4hf3
TitleActivity Enhancers of H64A Variant of Human Carbonic Anhydrase II Possess Multiple Binding Sites within and around the Enzyme Structure
ComponentsCarbonic anhydrase 2
KeywordsLYASE / hydration/dehydration / His64Ala
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 / regulation of intracellular pH / morphogenesis of an epithelium / 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 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
IMIDAZOLE / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1476 Å
AuthorsAggarwal, M. / McKenna, R.
CitationJournal: IUCrJ / Year: 2014
Title: Structural insight into activity enhancement and inhibition of H64A carbonic anhydrase II by imidazoles.
Authors: Aggarwal, M. / Kondeti, B. / Tu, C. / Maupin, C.M. / Silverman, D.N. / McKenna, R.
History
DepositionOct 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 12, 2014Group: Database references
Revision 1.2Aug 20, 2014Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,90911
Polymers29,2221
Non-polymers68710
Water5,314295
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.371, 41.484, 71.938
Angle α, β, γ (deg.)90.00, 104.38, 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: 29221.992 Da / Num. of mol.: 1 / Mutation: H64A
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: Chemical
ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Drops of 10 uL (0.3 mM protein; 100 mM small imidazole; 0.8 M sodium citrate; 50 mM Tris-HCl; pH 8.0) were equilibrated against the precipitant solution (1.6 M sodium citrate; 50 mM Tris-HCl; ...Details: Drops of 10 uL (0.3 mM protein; 100 mM small imidazole; 0.8 M sodium citrate; 50 mM Tris-HCl; pH 8.0) were equilibrated against the precipitant solution (1.6 M sodium citrate; 50 mM Tris-HCl; pH 8.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2011
RadiationMonochromator: Horizontal bent Si(111), asymmetrically cut with water coated Cu block
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.1476→19.88 Å / Num. obs: 85550

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7_650refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1476→19.88 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.11 / σ(F): 0 / Phase error: 15.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1719 1938 2.38 %
Rwork0.1583 --
obs0.1586 81455 94.05 %
all-86608 -
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.889 Å2 / ksol: 0.567 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5259 Å2-0 Å20.2971 Å2
2---0.839 Å20 Å2
3---1.3649 Å2
Refinement stepCycle: LAST / Resolution: 1.1476→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2044 0 46 295 2385
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112333
X-RAY DIFFRACTIONf_angle_d1.4013194
X-RAY DIFFRACTIONf_dihedral_angle_d13.177902
X-RAY DIFFRACTIONf_chiral_restr0.09335
X-RAY DIFFRACTIONf_plane_restr0.009423
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1476-1.17630.23981360.21895009X-RAY DIFFRACTION84
1.1763-1.20810.25921240.20645269X-RAY DIFFRACTION88
1.2081-1.24360.21421350.19575314X-RAY DIFFRACTION89
1.2436-1.28380.1951280.17945448X-RAY DIFFRACTION90
1.2838-1.32960.16351350.16495563X-RAY DIFFRACTION93
1.3296-1.38290.17141350.1635589X-RAY DIFFRACTION93
1.3829-1.44580.16371410.15345687X-RAY DIFFRACTION95
1.4458-1.5220.1631390.14585795X-RAY DIFFRACTION96
1.522-1.61730.1421470.14125813X-RAY DIFFRACTION97
1.6173-1.74210.1571420.13875936X-RAY DIFFRACTION98
1.7421-1.91730.15231360.13875979X-RAY DIFFRACTION99
1.9173-2.19440.16231480.14286059X-RAY DIFFRACTION100
2.1944-2.76360.16561450.15146053X-RAY DIFFRACTION100
2.7636-19.8830.17681470.16896003X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1285-0.3303-0.27960.8680.43941.46050.00290.0137-0.0725-0.0230.0226-0.21690.09670.21740.00820.04720.0065-0.00040.0931-0.00330.10278.5002-2.803216.9899
20.1216-0.18040.35010.4848-0.33781.2697-0.1534-0.20090.01550.13530.16790.06190.0202-0.1624-0.04750.07670.01830.00250.10540.00990.0618-13.5976-2.117430.8526
30.5274-0.01860.01850.42080.130.4775-0.00580.04430.0338-0.0099-0.01070.0251-0.0176-0.0141-0.0010.0481-0.0068-0.01070.0470.00280.049-12.83470.475213.7839
40.53570.12160.26270.36470.26450.3662-0.0011-0.02230.0405-0.0284-0.01580.0401-0.0182-0.00440.01240.0568-0.0044-0.00490.0392-0.00180.0369-11.2154.558318.1342
52.93021.8771-1.07341.7724-1.34951.1861-0.09090.1898-0.0198-0.23160.0940.11640.1294-0.05480.06550.083-0.0012-0.01720.0872-0.01320.0681-15.6707-6.6651-0.2375
60.99760.0095-0.27770.2961-0.0921.01890.0630.0459-0.0001-0.0408-0.00310.0179-0.0470.0168-0.04410.067-0.0085-0.01780.0703-0.00060.0593-17.0361-0.92116.6481
70.4521-0.05240.20050.40550.21440.54030.0123-0.0513-0.0150.0098-0.0041-0.01780.0257-0.024-0.00490.0387-0.0017-0.01050.03690.0040.0323-10.946-2.513921.9203
81.1012-0.5064-0.41790.6094-0.35481.04950.07040.2449-0.2085-0.14610.0270.00190.2250.24680.19770.07230.02690.00370.1701-0.04530.0609-4.9553-11.02661.0764
90.6212-0.14530.29870.40340.13590.68530.0036-0.0799-0.02630.06870.0346-0.04190.06280.0561-0.05410.0651-0.0036-0.0080.05720.0050.0533-5.2665-6.205924.1457
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 4:24)
2X-RAY DIFFRACTION2chain 'A' and (resseq 25:50)
3X-RAY DIFFRACTION3chain 'A' and (resseq 51:115)
4X-RAY DIFFRACTION4chain 'A' and (resseq 116:154)
5X-RAY DIFFRACTION5chain 'A' and (resseq 155:167)
6X-RAY DIFFRACTION6chain 'A' and (resseq 168:190)
7X-RAY DIFFRACTION7chain 'A' and (resseq 191:219)
8X-RAY DIFFRACTION8chain 'A' and (resseq 220:238)
9X-RAY DIFFRACTION9chain 'A' and (resseq 239:261)

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