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- PDB-3p4v: Human carbonic anhydrase II in complex with (+)-Xylariamide A -

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Basic information

Entry
Database: PDB / ID: 3p4v
TitleHuman carbonic anhydrase II in complex with (+)-Xylariamide A
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / Carbonic anhydrase / alpha type / LYASE-LYASE INHIBITOR complex
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 / regulation of intracellular pH / morphogenesis of an epithelium / 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
Chem-PMX / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsHofmann, A. / Nankervis, T. / Davis, R.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Natural Product-Based Phenols as Novel Probes for Mycobacterial and Fungal Carbonic Anhydrases.
Authors: Davis, R.A. / Hofmann, A. / Osman, A. / Hall, R.A. / Muhlschlegel, F.A. / Vullo, D. / Innocenti, A. / Supuran, C.T. / Poulsen, S.A.
History
DepositionOct 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)29,6823
Polymers29,2891
Non-polymers3932
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.312, 41.298, 72.427
Angle α, β, γ (deg.)90.00, 104.89, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET8c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PMX / 3-chloro-N-[(2E)-4-methoxy-4-oxobut-2-enoyl]-L-tyrosine / (+)-Xylariamide A


Mass: 327.717 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H14ClNO6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.5
Details: 3.2M (NH4)2SO4, 0.1M Glycine, pH 9.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953827 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953827 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 16550 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 17.6 Å2 / Rsym value: 0.051
Reflection shellResolution: 2→2.06 Å / Redundancy: 3.7 % / Num. unique all: 2420 / Rsym value: 0.075 / % possible all: 97

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIX(phenix.refine: 1.6.4_486)model building
PHENIX(phenix.refine: 1.6.4_486)refinement
XDSdata reduction
SCALAdata scaling
PHENIX1.6.4_486phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3HKN

3hkn


Resolution: 2→24.681 Å / SU ML: 0.21 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1594 5.08 %random
Rwork0.1619 ---
obs0.1641 16550 97.86 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.766 Å2 / ksol: 0.417 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8178 Å2-0 Å20.0382 Å2
2---0.0404 Å2-0 Å2
3---0.8582 Å2
Refinement stepCycle: LAST / Resolution: 2→24.681 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 23 157 2229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072139
X-RAY DIFFRACTIONf_angle_d1.0812905
X-RAY DIFFRACTIONf_dihedral_angle_d14.28790
X-RAY DIFFRACTIONf_chiral_restr0.078299
X-RAY DIFFRACTIONf_plane_restr0.007377
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.06450.21371440.144272497
2.0645-2.13830.25561340.1451269397
2.1383-2.22390.21641540.1656267797
2.2239-2.3250.24511340.1789266897
2.325-2.44750.25231480.1673272898
2.4475-2.60070.23411360.1743271798
2.6007-2.80120.22581490.1717272698
2.8012-3.08260.22421270.1799274799
3.0826-3.52760.18571840.1743268499
3.5276-4.44010.17381520.1378271299
4.4401-24.68270.16261320.1562269397

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