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- PDB-3czv: Crystal structure of the human carbonic anhydrase XIII in complex... -

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Basic information

Entry
Database: PDB / ID: 3czv
TitleCrystal structure of the human carbonic anhydrase XIII in complex with acetazolamide
ComponentsCarbonic anhydrase 13
KeywordsLYASE / Carbonic anhydrase / Protein-inhibitor complex / Metal-binding
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / 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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDi Fiore, A. / De Simone, G.
Citation
Journal: Proteins / Year: 2008
Title: Crystal structure of human carbonic anhydrase XIII and its complex with the inhibitor acetazolamide.
Authors: Di Fiore, A. / Monti, S.M. / Hilvo, M. / Parkkila, S. / Romano, V. / Scaloni, A. / Pedone, C. / Scozzafava, A. / Supuran, C.T. / De Simone, G.
#1: Journal: Proteins / Year: 1988
Title: Refined structure of human carbonic anhydrase II at 2.0 A resolution
Authors: Eriksson, A.E. / Jones, T.A. / Liljas, A.
History
DepositionApr 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 13
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9207
Polymers59,2532
Non-polymers6675
Water8,233457
1
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9143
Polymers29,6261
Non-polymers2882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0064
Polymers29,6261
Non-polymers3803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.030, 81.567, 112.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 13 / Carbonic anhydrase XIII / Carbonate dehydratase XIII / CA-XIII


Mass: 29626.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N1Q1, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 30% (w/v) PEG 4000, 0.2 M Ammonium acetate, 0.1 M Sodium citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 33948 / Num. obs: 33948 / % possible obs: 90.3 % / Redundancy: 7.8 % / Rsym value: 0.061 / Net I/σ(I): 26.9
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 3.5 / Num. unique all: 2652 / Rsym value: 0.414 / % possible all: 71.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Native human carbonic anhydrase XIII

Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1628 -RANDOM
Rwork0.178 ---
all-33948 --
obs-32808 87.8 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4105 0 34 457 4596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4

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