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- PDB-1cvd: STRUCTURAL CONSEQUENCES OF REDESIGNING A PROTEIN-ZINC BINDING SITE -

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Basic information

Entry
Database: PDB / ID: 1cvd
TitleSTRUCTURAL CONSEQUENCES OF REDESIGNING A PROTEIN-ZINC BINDING SITE
ComponentsCARBONIC ANHYDRASE IICarbonic anhydrase
KeywordsLYASE(OXO-ACID)
Function / homologyCarbonic anhydrase, alpha-class / Reversible hydration of carbon dioxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Alpha-carbonic anhydrases profile. / Alpha-carbonic anhydrases signature. / Eukaryotic-type carbonic anhydrase / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Carbonic anhydrase, alpha-class, conserved site ...Carbonic anhydrase, alpha-class / Reversible hydration of carbon dioxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Alpha-carbonic anhydrases profile. / Alpha-carbonic anhydrases signature. / Eukaryotic-type carbonic anhydrase / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Carbonic anhydrase, alpha-class, conserved site / positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / secretion / regulation of anion transport / carbon dioxide transport / angiotensin-activated signaling pathway / regulation of chloride transport / arylesterase activity / regulation of intracellular pH / positive regulation of osteoclast differentiation / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / response to pH / cellular response to fluid shear stress / carbonic anhydrase / carbonate dehydratase activity / response to steroid hormone / odontogenesis of dentin-containing tooth / response to zinc ion / positive regulation of bone resorption / microvillus / bicarbonate transport / kidney development / apical part of cell / myelin sheath / basolateral plasma membrane / response to estrogen / axon / zinc ion binding / extracellular exosome / plasma membrane / cytosol / cytoplasm / Carbonic anhydrase 2
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / 2.2 Å resolution
AuthorsIppolito, J.A. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 1994
Title: Structural consequences of redesigning a protein-zinc binding site.
Authors: Ippolito, J.A. / Christianson, D.W.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 21, 1994 / Release: Dec 20, 1994
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 20, 1994Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Nov 29, 2017Structure modelDerived calculations / Otherpdbx_database_status / struct_conf / struct_conf_type_pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6962
Polyers28,6301
Non-polymers651
Water2,036113
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)42.700, 41.700, 73.000
Angle α, β, γ (deg.)90.00, 104.60, 90.00
Int Tables number4
Space group name H-MP 1 21 1
Atom site foot note1: CIS PROLINE - PRO 30 / 2: CIS PROLINE - PRO 202

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Components

#1: Protein/peptide CARBONIC ANHYDRASE II / Carbonic anhydrase


Mass: 28630.307 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Formula: H2O / Water
Compound detailsSECONDARY STRUCTURE ELEMENTS WERE DEFINED USING THE PROGRAM *DSSP* (W. KABSCH, C. SANDER, ...SECONDARY STRUCTURE ELEMENTS WERE DEFINED USING THE PROGRAM *DSSP* (W. KABSCH, C. SANDER, BIOPOLYMERS, V. 22, P. 2577, 1983).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.2 / Density percent sol: 43.97 %
Crystal grow
*PLUS
Temp: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop / Details: Alexander, R.S., (1991) Biochemistry, 30, 11064.
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol IDChemical formula
10.3 mMenzyme1drop
250 mMTris-HCl1drop
3150 mM1dropNaCl
43 mM1drop NaN3
51.75-2.5 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
D resolution high: 2.2 Å / Number obs: 10673 / Number measured all: 18890 / Rmerge I obs: 0.088

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefineSigma I: 2
Least-squares processR factor obs: 0.184 / Highest resolution: 2.2 Å / Lowest resolution: 7 Å / Number reflection obs: 10014
Refine hist #LASTHighest resolution: 2.2 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 2025 / Nucleic acid: 0 / Ligand: 1 / Solvent: 113 / Total: 2139
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.030
X-RAY DIFFRACTIONp_angle_d0.0330.050
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.3601.000
X-RAY DIFFRACTIONp_mcangle_it0.6181.500
X-RAY DIFFRACTIONp_scbond_it0.3421.000
X-RAY DIFFRACTIONp_scangle_it0.5871.500
X-RAY DIFFRACTIONp_plane_restr0.0060.020
X-RAY DIFFRACTIONp_chiral_restr0.0870.150
X-RAY DIFFRACTIONp_singtor_nbd0.1870.500
X-RAY DIFFRACTIONp_multtor_nbd0.2250.500
X-RAY DIFFRACTIONp_xhyhbond_nbd0.2060.500
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.10015.00
X-RAY DIFFRACTIONp_staggered_tor16.0015.00
X-RAY DIFFRACTIONp_orthonormal_tor24.5015.00
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.184

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