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- PDB-5jmz: Carbonic Anhydrase IX-mimic IN Complex WITH U-NO2 -

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Basic information

Entry
Database: PDB / ID: 5jmz
TitleCarbonic Anhydrase IX-mimic IN Complex WITH U-NO2
ComponentsCarbonic anhydrase 2
KeywordsLYASE/LYASE INHIBITOR / CAIX 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-AYX / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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)CA165284-03S United States
CitationJournal: To Be Published
Title: Carbonic Anhydrase IX-mimic IN Complex WITH U-NO2
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)29,3244
Polymers28,8441
Non-polymers4803
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.018, 41.410, 72.070
Angle α, β, γ (deg.)90.000, 103.720, 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: 28844.465 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
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE / Dimethyl sulfoxide


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Chemical ChemComp-AYX / 4-{[(3-nitrophenyl)carbamoyl]amino}benzenesulfonamide


Mass: 336.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H12N4O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 41.75 %
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: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 18546 / % possible obs: 96.6 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.038 / Rrim(I) all: 0.069 / Χ2: 0.916 / Net I/av σ(I): 19.378 / Net I/σ(I): 18.3 / Num. measured all: 61102
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.933.20.1988710.9320.1280.2361.02894.1
1.93-1.973.30.1579070.9630.1010.1870.89794.3
1.97-2.013.30.1458850.9720.0930.1730.90894.1
2.01-2.053.30.1268790.9760.0810.150.92994.8
2.05-2.093.30.1129350.9820.0720.1340.93395.4
2.09-2.143.30.0989010.9850.0630.1170.89495.1
2.14-2.193.30.0959390.9830.0610.1131.00495.7
2.19-2.253.30.0788830.990.050.0930.82595.4
2.25-2.323.30.0769250.9870.0490.0910.9196.2
2.32-2.393.30.0739130.990.0470.0870.89796.6
2.39-2.483.30.0699300.9910.0450.0830.89696.7
2.48-2.583.30.0679350.990.0440.080.97396.9
2.58-2.693.30.0589210.9920.0380.070.85397.6
2.69-2.843.30.0559440.9920.0350.0650.90197.7
2.84-3.013.30.0499510.9940.0320.0590.82297.3
3.01-3.253.30.0479440.9940.0310.0570.86598.7
3.25-3.573.30.0459370.9940.030.0540.86498.4
3.57-4.083.30.0459660.9950.0290.0540.88698.8
4.08-5.133.30.0489680.9930.0310.0570.93899
5.13-203.10.05110120.9830.0340.0621.09799.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(1.10pre_2097: ???)refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.915 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1952 926 5 %
Rwork0.1615 --
obs0.1632 18533 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.38 Å2 / Biso mean: 21.6614 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 1.9→19.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 28 170 2240
Biso mean--37.28 28.66 -
Num. residues----257
Refinement TLS params.Method: refined / Origin x: -5.327 Å / Origin y: -0.287 Å / Origin z: 86.243 Å
111213212223313233
T0.0255 Å20.0035 Å20.0032 Å2-0.024 Å20.0001 Å2--0.0233 Å2
L0.3928 °20.0593 °20.1078 °2-0.3775 °20.0946 °2--0.3306 °2
S-0.0144 Å °-0.0278 Å °0.0262 Å °-0.0459 Å °0.0071 Å °-0.002 Å °-0.0033 Å °0.0158 Å °0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 261
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION1A401 - 570
4X-RAY DIFFRACTION1A302
5X-RAY DIFFRACTION1A303

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