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- PDB-6xvh: carbonic anhydrase with bound arylsulfonamide- boronic acid -

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Basic information

Entry
Database: PDB / ID: 6xvh
Titlecarbonic anhydrase with bound arylsulfonamide- boronic acid
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / carbonic anhydrase with bound arylsulfonamide- boronic 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 / regulation of chloride transport / arylesterase activity / 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 / regulation of chloride transport / arylesterase activity / 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, 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
(4-sulfamoylphenyl)boronic acid / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPerez, C. / Zhang, B.
CitationJournal: To Be Published
Title: An easy to assemble, fully modulable, selectiv and colorimetric artificial bio-sensor for fingerprintting the recognition of neurotransmitters
Authors: Rossel, T. / Perez, C. / Zhang, B. / Gobat, R.
History
DepositionJan 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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)29,1993
Polymers28,9331
Non-polymers2662
Water3,783210
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.310, 41.360, 72.120
Angle α, β, γ (deg.)90.000, 104.220, 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: 28932.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-O3B / (4-sulfamoylphenyl)boronic acid


Mass: 201.008 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8BNO4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 41.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: Tris, Ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→29.123 Å / Num. obs: 41104 / % possible obs: 86.4 % / Redundancy: 3.23 % / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.065 / Χ2: 1.242 / Net I/σ(I): 11.89 / Num. measured all: 132782
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.75-1.81.9340.7111.392029356410490.4410.9629.4
1.8-1.852.1820.5582.294275345819590.5690.74156.7
1.85-1.92.3210.4513.095221328522490.7220.5968.5
1.9-1.962.4970.3744.196386321125570.790.47779.6
1.96-2.022.8930.2985.428395319529020.8910.36890.8
2.02-2.13.5540.2667.1210636299829930.9380.31499.8
2.1-2.173.6250.2058.6110629295429320.9560.24199.3
2.17-2.263.6360.1699.7910025279027570.9690.19998.8
2.26-2.363.5720.13810.299642273126990.970.16398.8
2.36-2.483.4870.11911.218858258025400.9780.14198.4
2.48-2.613.2640.098127810245123930.9810.11797.6
2.61-2.773.6440.08513.878454232923200.9880.199.6
2.77-2.963.5880.07115.297812221021770.990.08498.5
2.96-3.23.5010.06117.316900199219710.9930.07298.9
3.2-3.513.3540.05119.036124188918260.9920.06196.7
3.51-3.923.1930.04621.875137167816090.9940.05595.9
3.92-4.533.5620.04126.055300150314880.9970.04899
4.53-5.543.4660.03628.724280125912350.9970.04398.1
5.54-7.843.2340.03330.1630019739280.9960.0495.4
7.84-29.1233.5920.02736.8418685275200.9990.03198.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BN1

1bn1


Resolution: 1.8→29.123 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.27
RfactorNum. reflection% reflection
Rfree0.2451 1070 5.12 %
Rwork0.1932 --
obs0.1958 20901 92.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 74.09 Å2 / Biso mean: 32.3301 Å2 / Biso min: 13.99 Å2
Refinement stepCycle: final / Resolution: 1.8→29.123 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 14 210 2273
Biso mean--30 36.57 -
Num. residues----257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062114
X-RAY DIFFRACTIONf_angle_d0.8572869
X-RAY DIFFRACTIONf_chiral_restr0.054299
X-RAY DIFFRACTIONf_plane_restr0.006373
X-RAY DIFFRACTIONf_dihedral_angle_d12.4841246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8820.3858930.2749166563
1.882-1.98120.26091230.2268217481
1.9812-2.10520.26021310.2094261698
2.1052-2.26770.2671500.21062642100
2.2677-2.49580.27911460.2189266699
2.4958-2.85670.26211400.2121266999
2.8567-3.59810.22471330.1954268399
3.5981-29.1230.22581540.1661271698
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.176-0.21530.20810.2729-0.23780.33170.0011-0.055-0.3322-0.2306-0.2347-0.48010.07140.2888-0.05550.18350.04630.04950.3680.00020.369529.9621-5.303914.5656
20.2394-0.16690.13170.1438-0.07090.2064-0.1787-0.386-0.06330.2490.1271-0.19630.11560.15120.00150.24660.0307-0.01350.32650.00770.251418.2205-4.592329.149
30.2617-0.16680.06510.3772-0.00940.0693-0.039-0.13180.31920.01770.08150.0735-0.1084-0.03510.00030.26670.0206-0.00090.35670.01430.34481.70243.706817.7589
40.61440.03590.03310.25440.16150.6463-0.0329-0.01270.0427-0.0676-0.00040.03820.00770.011600.2221-0.0052-0.00290.18480.00990.229.4782-1.351915.4274
50.7394-0.0975-0.07550.8935-0.14050.88960.01130.0130.0339-0.08990.03190.07570.0586-0.034500.1787-0.0055-0.00930.17130.00470.17279.7878-2.552212.4503
60.3212-0.2810.14560.6106-0.12570.1118-0.1272-0.1894-0.0937-0.02710.0883-0.03440.16460.0125-0.00010.2310.0411-0.00650.33370.01190.22615.8023-7.25824.0617
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 4 through 19 )A4 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 39 )A20 - 39
3X-RAY DIFFRACTION3chain 'A' and (resid 40 through 61 )A40 - 61
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 115 )A62 - 115
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 238 )A116 - 238
6X-RAY DIFFRACTION6chain 'A' and (resid 239 through 261 )A239 - 261

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