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- PDB-6pea: High Resolution Apo Carbonic Anhydrase II -

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Basic information

Entry
Database: PDB / ID: 6pea
TitleHigh Resolution Apo Carbonic Anhydrase II
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Apo / Metal Substitution
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 activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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 / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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
Similarity search - Domain/homology
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsAndring, J.T. / McKenna, R.
CitationJournal: Iucrj / Year: 2020
Title: Structure and mechanism of copper-carbonic anhydrase II: a nitrite reductase.
Authors: Andring, J.T. / Kim, C.U. / McKenna, R.
History
DepositionJun 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4112
Polymers29,2891
Non-polymers1221
Water3,801211
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.289, 41.305, 72.039
Angle α, β, γ (deg.)90.000, 104.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.1 Å3/Da / Density % sol: 41.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.6M NaCitrate, 50mM Tris

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.36→39.87 Å / Num. obs: 49512 / % possible obs: 94.5 % / Redundancy: 3.3 % / Biso Wilson estimate: 11.91 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Rpim(I) all: 0.014 / Rrim(I) all: 0.026 / Net I/σ(I): 20 / Num. measured all: 163103 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.36-1.382.40.183378415780.9380.1410.2333.761
7.42-39.873.30.012117635210.0080.01541.799

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ks3

3ks3


Resolution: 1.36→39.87 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.31
RfactorNum. reflection% reflection
Rfree0.1643 2005 3.98 %
Rwork0.1485 --
obs0.1492 50384 95.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.57 Å2 / Biso mean: 18.8117 Å2 / Biso min: 6.33 Å2
Refinement stepCycle: final / Resolution: 1.36→39.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 8 211 2278
Biso mean--35.83 26.71 -
Num. residues----258
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072237
X-RAY DIFFRACTIONf_angle_d1.2953051
X-RAY DIFFRACTIONf_chiral_restr0.089313
X-RAY DIFFRACTIONf_plane_restr0.013401
X-RAY DIFFRACTIONf_dihedral_angle_d14.707833
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3556-1.38950.21831030.19452454255768
1.3895-1.42710.20851340.17733415354995
1.4271-1.46910.18451560.16383493364998
1.4691-1.51650.18681320.15973534366698
1.5165-1.57070.16271550.1623451360697
1.5707-1.63360.17631500.15073481363198
1.6336-1.7080.18231400.15373532367298
1.708-1.7980.15581450.14953534367998
1.798-1.91070.16311420.14553485362797
1.9107-2.05820.15491490.14213577372699
2.0582-2.26530.14811440.13793561370599
2.2653-2.5930.15131510.14363570372199
2.593-3.26670.17121520.15273629378199
3.2667-41.020.161520.1433663381599
Refinement TLS params.Method: refined / Origin x: -9.657 Å / Origin y: -1.764 Å / Origin z: 16.06 Å
111213212223313233
T0.0688 Å2-0.0039 Å20.0016 Å2-0.0697 Å20.0016 Å2--0.0645 Å2
L0.6336 °2-0.0181 °20.0422 °2-0.8644 °20.1723 °2--0.4688 °2
S-0.0208 Å °-0.0275 Å °0.0132 Å °-0.0849 Å °0.0279 Å °-0.0139 Å °-0.0235 Å °0.0113 Å °0.0139 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:261 OR RESID 401:611 OR RESID 301:301 ) )A3 - 261
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:261 OR RESID 401:611 OR RESID 301:301 ) )A401 - 611
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:261 OR RESID 401:611 OR RESID 301:301 ) )A301

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