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- PDB-1crm: STRUCTURE AND FUNCTION OF CARBONIC ANHYDRASES -

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Basic information

Entry
Database: PDB / ID: 1crm
TitleSTRUCTURE AND FUNCTION OF CARBONIC ANHYDRASES
ComponentsCARBONIC ANHYDRASE ICarbonic anhydrase
KeywordsLYASE (OXO-ACID)
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / 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
HYDROSULFURIC ACID / : / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsYadava, V.S. / Kannan, K.K.
Citation
Journal: Biomolecular Structure, Conformation, Function and Evolution
Year: 1981
Title: Structure and Function of Carbonic Anhydrases
Authors: Kannan, K.K.
#1: Journal: J.Mol.Biol. / Year: 1972
Title: Structure of Human Carbonic Anhydrase B. I. Crystallization and Heavy Atom Modification
Authors: Kannan, K.K. / Fridborg, K. / Bergsten, P.C. / Liljas, A. / Lovgren, S. / Petef, M. / Strandberg, B. / Waara, I. / Alder, L. / Falkbring, S.O. / Gothe, P.O. / Nyman, P.O.
History
DepositionMar 4, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE ...SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. STRANDS 1 - 3 AND 5 - 10 OF AS1 AND BS1 ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6968
Polymers28,7891
Non-polymers9077
Water4,720262
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.850, 75.310, 37.759
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: CIS PROLINE - PRO 30 / 2: CIS PROLINE - PRO 202

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Components

#1: Protein CARBONIC ANHYDRASE I / Carbonic anhydrase


Mass: 28789.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00915, carbonic anhydrase
#2: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE / Hydrogen sulfide


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 262 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSECONDARY STRUCTURE ELEMENTS AND TURNS HAVE BEEN IDENTIFIED USING W.KABSCH AND C.SANDER'S ALGORITHM ...SECONDARY STRUCTURE ELEMENTS AND TURNS HAVE BEEN IDENTIFIED USING W.KABSCH AND C.SANDER'S ALGORITHM (PROGRAM *DSSP*; AUTHORS W.KABSCH AND C.SANDER).
Nonpolymer detailsTHE HG2+ WHICH REPLACES ZN2+ IS 0.5A AWAY FROM ZN2+ POSITION IN THE NATIVE ENZYME. RESIDUES SER 188 ...THE HG2+ WHICH REPLACES ZN2+ IS 0.5A AWAY FROM ZN2+ POSITION IN THE NATIVE ENZYME. RESIDUES SER 188 AND LEU 189 HAVE MOVED BY LARGE DISTANCE COMPARED TO THE NATIVE STRUCTURE. THE WATER MOLECULE OBSERVED AT FOURTH COORDINATION OF ZN2+ IN THE NATIVE ENZYME IS NOT PRESENT IN THIS COMPLEX AND IS PROBABLY A REASON FOR THE LOSS OF ENZYME ACTIVITY WHEN ZN2+ IS REPLACED BY HG2+.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.11 %

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
PROLSQrefinement
TOMrefinement
PIKSOLrefinement
RefinementResolution: 2→8 Å / σ(F): 2
Details: THE HG2+ BOUND TO CYS 212 IS DISORDERED WITH TWO SITES FOR HG2+ SEPARATED BY ABOUT 1.6 ANGSTROMS. CYS 212 SHOWS MULTIPLE CONFORMATIONS. THESE FEATURES ARE CLEARLY SEEN IN (FO - FC) MAP.
RfactorNum. reflection
obs0.177 14584
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2009 0 7 262 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0320.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0130.02
X-RAY DIFFRACTIONp_chiral_restr0.1540.15
X-RAY DIFFRACTIONp_singtor_nbd0.0410.05
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.42.4
X-RAY DIFFRACTIONp_staggered_tor17.417.4
X-RAY DIFFRACTIONp_orthonormal_tor31.231.2
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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