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- PDB-1urt: MURINE CARBONIC ANHYDRASE V -

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Basic information

Entry
Database: PDB / ID: 1urt
TitleMURINE CARBONIC ANHYDRASE V
ComponentsCARBONIC ANHYDRASE V
KeywordsLYASE / ZINC / MITOCHONDRION / TRANSIT PEPTIDE
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / gluconeogenesis / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / mitochondrion / zinc ion binding / 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
Carbonic anhydrase 5A, mitochondrial
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsBoriack-Sjodin, P.A. / Christianson, D.W.
Citation
Journal: Biochemistry / Year: 1996
Title: Structure-based design of an intramolecular proton transfer site in murine carbonic anhydrase V.
Authors: Heck, R.W. / Boriack-Sjodin, P.A. / Qian, M. / Tu, C. / Christianson, D.W. / Laipis, P.J. / Silverman, D.N.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: Structure Determination of Murine Mitochondrial Carbonic Anhydrase V at 2.45-A Resolution: Implications for Catalytic Proton Transfer and Inhibitor Design
Authors: Boriack-Sjodin, P.A. / Heck, R.W. / Laipis, P.J. / Silverman, D.N. / Christianson, D.W.
#2: Journal: J.Biol.Chem. / Year: 1994
Title: Catalytic Properties of Mouse Carbonic Anhydrase V
Authors: Heck, R.W. / Tanhauser, S.M. / Manda, R. / TU, C. / Laipis, P.J. / Silverman, D.N.
History
DepositionJul 3, 1996Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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_conn.ptnr2_label_seq_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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE V
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2702
Polymers28,2051
Non-polymers651
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.090, 67.520, 48.860
Angle α, β, γ (deg.)90.00, 107.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CARBONIC ANHYDRASE V / CARBONATE DEHYDROGENASE (MCAVC)


Mass: 28204.646 Da / Num. of mol.: 1
Mutation: Y64H, F65A, TRUNCATION OF MITOCHONDRIAL LEADER SEQUENCE AND FIRST 21 RESIDUES
Source method: isolated from a genetically manipulated source
Details: MURINE CARBONIC ANHYDRASE V / Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/CJ / Cell line: BL21 / Gene: MCA5C Y64H F65A / Organ: LIVER / Organelle: MITOCHONDRIA / Plasmid: PET31 T7 / Gene (production host): MCA5C Y64H F65A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P23589, 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


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56 %
Crystal
*PLUS
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
250 mMTris1drop
32.0 mMsucrose monolaurate1drop
416-12 %PEG80001drop
50.2 Msodium acetate1drop
60.1 Msodium cacodylate1drop
716-12 %PEG80001reservoir
80.2 Msodium acetate1reservoir
90.1 Msodium cacodylate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 2, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 6759 / % possible obs: 86.9 % / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 6760 / % possible obs: 87 % / Num. measured all: 19846

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
MOSFLMdata reduction
X-PLORphasing
RefinementResolution: 2.8→6.5 Å / σ(F): 3
RfactorNum. reflection
Rfree0.241 -
Rwork0.137 -
obs0.137 5565
Refinement stepCycle: LAST / Resolution: 2.8→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 1 32 1925
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 6174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg25.6
X-RAY DIFFRACTIONx_improper_angle_deg1.3

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