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- PDB-5jn7: Carbonic Anhydrase II In Complex WITH U-CH3 -

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Basic information

Entry
Database: PDB / ID: 5jn7
TitleCarbonic Anhydrase II In Complex WITH U-CH3
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / CA inhibitors / pH regulation / cancer therapeutics / transmembrane / 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-6LU / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.517 Å
AuthorsMcKenna, R. / Mboge, M.Y. / Mahon, B.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)CA165284-03S1 United States
CitationJournal: To Be Published
Title: Carbonic Anhydrase II In Complex WITH U-CH3
Authors: McKenna, R. / Mboge, M.Y. / Mahon, B.P.
History
DepositionApr 29, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6447
Polymers28,9331
Non-polymers7116
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.308, 41.378, 72.036
Angle α, β, γ (deg.)90.000, 104.120, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 28932.641 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 K-12 (bacteria) / References: UniProt: P00918, carbonic anhydrase

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Non-polymers , 5 types, 214 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6LU / 4-{[(3,5-dimethylphenyl)carbamoyl]amino}benzene-1-sulfonamide


Mass: 319.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N3O3S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.6 M Na-Citrate, 50 mM Tris, pH 7.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.52→50 Å / Num. obs: 34770 / % possible obs: 92.2 % / Redundancy: 7.4 % / Biso Wilson estimate: 12.35 Å2 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Χ2: 0.94 / Net I/av σ(I): 28.588 / Net I/σ(I): 8.8 / Num. measured all: 257545
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.52-1.5560.48910730.8960.2080.5331.05757.8
1.55-1.576.30.41412710.9250.1720.4490.73967.1
1.57-1.66.50.37113970.9330.1540.4030.874.6
1.6-1.646.50.3616490.9190.1490.390.83489.2
1.64-1.677.10.31517900.9540.1250.340.72795.5
1.67-1.717.40.26717900.9690.1050.2870.76995.6
1.71-1.757.50.22817750.9780.0880.2450.78895.5
1.75-1.87.60.20518500.9840.0790.2190.89196.8
1.8-1.867.70.1717970.9890.0650.1820.96395.8
1.86-1.927.70.13317930.9910.0510.1430.90196.4
1.92-1.987.70.12318390.9930.0470.1321.05297.3
1.98-2.067.70.09218190.9960.0350.0990.92397.1
2.06-2.167.80.08218010.9970.0310.0870.92897
2.16-2.277.70.07518370.9970.0290.080.98197.5
2.27-2.417.70.06218510.9970.0240.0660.82897.8
2.41-2.67.70.05718620.9980.0220.0610.80498.1
2.6-2.867.70.05218610.9980.020.0560.84797.7
2.86-3.277.60.04918810.9990.0190.0520.98498.6
3.27-4.137.60.04518870.9980.0180.0481.1299.1
4.13-507.30.05519470.9980.0220.0591.72898.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.517→29.134 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1892 1735 5 %
Rwork0.1654 53179 -
obs0.1666 34658 76.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.59 Å2 / Biso mean: 17.9859 Å2 / Biso min: 7.5 Å2
Refinement stepCycle: final / Resolution: 1.517→29.134 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 41 208 2298
Biso mean--28.7 25.52 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082151
X-RAY DIFFRACTIONf_angle_d1.3882916
X-RAY DIFFRACTIONf_chiral_restr0.076299
X-RAY DIFFRACTIONf_plane_restr0.014376
X-RAY DIFFRACTIONf_dihedral_angle_d10.7082187
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5166-1.54280.3296510.2451969102028
1.5428-1.57080.2483590.21761172123133
1.5708-1.6010.2707640.20361343140738
1.601-1.63370.2351940.20551594168846
1.6337-1.66920.2083990.19571822192152
1.6692-1.7080.22651000.16642008210857
1.708-1.75080.18041150.16112179229463
1.7508-1.79810.21681330.15532515264871
1.7981-1.8510.21011300.15562766289678
1.851-1.91070.17191620.16322902306485
1.9107-1.9790.19551650.16783187335291
1.979-2.05820.17961690.16163315348495
2.0582-2.15190.20371700.16223371354197
2.1519-2.26530.20041950.16493387358298
2.2653-2.40710.18711740.17423417359198
2.4071-2.59290.20841850.17983453363898
2.5929-2.85360.20641860.18173427361398
2.8536-3.26610.19261770.1823458363599
3.2661-4.1130.17311750.14773456363199
4.113-29.13980.15481980.14233438363699
Refinement TLS params.Method: refined / Origin x: -6.0113 Å / Origin y: -2.1058 Å / Origin z: 85.6948 Å
111213212223313233
T0.0768 Å2-0.0006 Å20.0006 Å2-0.0745 Å20.0014 Å2--0.0805 Å2
L0.5364 °2-0.0986 °20.003 °2-0.3717 °20.0134 °2--0.5121 °2
S0.0028 Å °-0.0379 Å °0.0152 Å °-0.0166 Å °-0.006 Å °-0.001 Å °0.0053 Å °0.0217 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 261
2X-RAY DIFFRACTION1allB262
3X-RAY DIFFRACTION1allD1 - 254
4X-RAY DIFFRACTION1allC1
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1 - 3

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