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- PDB-1cnb: COMPENSATORY PLASTIC EFFECTS IN THE REDESIGN OF PROTEIN-ZINC BIND... -

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Basic information

Entry
Database: PDB / ID: 1cnb
TitleCOMPENSATORY PLASTIC EFFECTS IN THE REDESIGN OF PROTEIN-ZINC BINDING SITES
ComponentsCARBONIC ANHYDRASE IICarbonic anhydrase
KeywordsLYASE(OXO-ACID)
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 / morphogenesis of an epithelium / regulation of intracellular pH / 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
BETA-MERCAPTOETHANOL / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
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.
History
DepositionJun 13, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 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

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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)29,2012
Polymers29,1231
Non-polymers781
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
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-MP1211
Atom site foot note1: CIS PROLINE - PRO 30 / 2: CIS PROLINE - PRO 202

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Components

#1: Protein CARBONIC ANHYDRASE II / Carbonic anhydrase


Mass: 29122.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
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: 2.16 Å3/Da / Density % sol: 43.01 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, sitting drop / Details: Alexander, R.S., (1991) Biochemistry, 30, 11064.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.3 mMenzyme1drop
250 mMTris-HCl1drop
3150 mM1dropNaCl
43 mM1dropNaN3
51.75-2.5 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.35 Å / Num. obs: 8563 / Num. measured all: 18847 / Rmerge(I) obs: 0.075

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.35→7 Å / σ(I): 2 /
RfactorNum. reflection
obs0.182 7387
Refinement stepCycle: LAST / Resolution: 2.35→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 0 139 2164
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.03
X-RAY DIFFRACTIONp_angle_d0.0380.06
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.3161
X-RAY DIFFRACTIONp_mcangle_it0.5721.5
X-RAY DIFFRACTIONp_scbond_it0.2311
X-RAY DIFFRACTIONp_scangle_it0.4171.5
X-RAY DIFFRACTIONp_plane_restr0.0050.02
X-RAY DIFFRACTIONp_chiral_restr0.0820.15
X-RAY DIFFRACTIONp_singtor_nbd0.2020.5
X-RAY DIFFRACTIONp_multtor_nbd0.2550.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.250.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor1.815
X-RAY DIFFRACTIONp_staggered_tor15.215
X-RAY DIFFRACTIONp_orthonormal_tor25.715
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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