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- PDB-6gcy: Joint neutron and x-ray crystal structure of human carbonic anhyd... -

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Basic information

Entry
Database: PDB / ID: 6gcy
TitleJoint neutron and x-ray crystal structure of human carbonic anhydrase IX mimic (saccharin-sugar conjugate complex)
ComponentsCarbonic anhydrase 2
KeywordsLYASE / proton transfer / carbonic anhydrase
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-3QR / DEUTERATED WATER / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / SYNCHROTRON / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsFisher, S.Z. / Koruza, K.
CitationJournal: J. Struct. Biol. / Year: 2019
Title: Using neutron crystallography to elucidate the basis of selective inhibition of carbonic anhydrase by saccharin and a derivative.
Authors: Koruza, K. / Mahon, B.P. / Blakeley, M.P. / Ostermann, A. / Schrader, T.E. / McKenna, R. / Knecht, W. / Fisher, S.Z.
History
DepositionApr 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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)29,7093
Polymers29,2011
Non-polymers5082
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24400 Å2
ΔGint30 kcal/mol
Surface area12530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.610, 41.940, 72.770
Angle α, β, γ (deg.)90.00, 104.01, 90.00
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: 29200.887 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / 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-3QR / [1-(1,1-dioxido-3-oxo-2,3-dihydro-1,2-benzothiazol-6-yl)-1H-1,2,3-triazol-4-yl]methyl alpha-L-idopyranoside


Mass: 442.401 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H18N4O9S
#4: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.07 % / Description: Thick rods.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.2 M sodium citrate, 0.1 M Tris pH 8.5 in Hampton sandwich box set-ups. Drops were 150-250 uL and we set-up in a 1:1 ratio. To get the complex with SGC ligand we did "dry co-crystallization".

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF BM30A11.04
NUCLEAR REACTORFRM II BIODIFF22.66
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 15, 2016
MAATEL IMAGINE2IMAGE PLATEMar 1, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMneutron2
Radiation wavelength
IDWavelength (Å)Relative weight
11.041
22.661
Reflection

Entry-ID: 6GCY

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)
1.3-366005697.67.30.051122.3
2-5016153932.30.16823.9
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID
1.3-1.40.5241
2-2.060.4692

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
Refinement

SU ML: 0.1 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 19.66 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4riu

4riu

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.3-20.97X-RAY DIFFRACTION0.15510.14780.1484360160047697.6211.37
2-29.009NEUTRON DIFFRACTION0.21220.1910.19311603161429.9392.9521.5
Refinement stepCycle: LAST / Resolution: 1.3→20.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 31 209 2292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095181
X-RAY DIFFRACTIONf_angle_d1.1738899
X-RAY DIFFRACTIONf_dihedral_angle_d19.9921351
X-RAY DIFFRACTIONf_chiral_restr0.092335
X-RAY DIFFRACTIONf_plane_restr0.006907
NEUTRON DIFFRACTIONf_bond_d0.0095181
NEUTRON DIFFRACTIONf_angle_d1.1738899
NEUTRON DIFFRACTIONf_dihedral_angle_d19.9921351
NEUTRON DIFFRACTIONf_chiral_restr0.092335
NEUTRON DIFFRACTIONf_plane_restr0.006907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31710.2382890.21932060X-RAY DIFFRACTION92
1.3171-1.33510.22261090.19562128X-RAY DIFFRACTION96
1.3351-1.35420.20621130.19252179X-RAY DIFFRACTION97
1.3542-1.37440.19951000.19712152X-RAY DIFFRACTION95
1.3744-1.39590.2188990.19212190X-RAY DIFFRACTION97
1.3959-1.41880.1851000.18812163X-RAY DIFFRACTION96
1.4188-1.44320.18611070.18452167X-RAY DIFFRACTION98
1.4432-1.46950.2257920.182170X-RAY DIFFRACTION96
1.4695-1.49770.18971110.17872219X-RAY DIFFRACTION98
1.4977-1.52830.20631190.1752143X-RAY DIFFRACTION96
1.5283-1.56150.1997880.17432225X-RAY DIFFRACTION98
1.5615-1.59780.21321170.16472146X-RAY DIFFRACTION97
1.5978-1.63780.1889990.16772204X-RAY DIFFRACTION97
1.6378-1.6820.18811060.17222240X-RAY DIFFRACTION99
1.682-1.73150.18041100.16812167X-RAY DIFFRACTION98
1.7315-1.78740.19351070.16622229X-RAY DIFFRACTION98
1.7874-1.85120.16671080.16172215X-RAY DIFFRACTION98
1.8512-1.92530.15071070.15372240X-RAY DIFFRACTION99
1.9253-2.01280.17151160.14842206X-RAY DIFFRACTION99
2.0128-2.11890.16932110.14712138X-RAY DIFFRACTION99
2.1189-2.25150.15072290.1462110X-RAY DIFFRACTION99
2.2515-2.42510.14312120.14432144X-RAY DIFFRACTION99
2.4251-2.66870.15542410.1392135X-RAY DIFFRACTION99
2.6687-3.05380.16192290.13642153X-RAY DIFFRACTION99
3.0538-3.84360.14212390.11982147X-RAY DIFFRACTION100
3.8436-20.97270.1222430.11232176X-RAY DIFFRACTION98
1.9895-2.05370.2973900.2704887NEUTRON DIFFRACTION63
2.0537-2.12710.27811520.25691316NEUTRON DIFFRACTION93
2.1271-2.21220.29151480.24521368NEUTRON DIFFRACTION96
2.2122-2.31290.27061320.24021307NEUTRON DIFFRACTION92
2.3129-2.43470.24721480.21471307NEUTRON DIFFRACTION94
2.4347-2.58720.19741560.19491394NEUTRON DIFFRACTION98
2.5872-2.78680.19291550.19081381NEUTRON DIFFRACTION97
2.7868-3.0670.21571470.17281389NEUTRON DIFFRACTION98
3.067-3.51010.18771580.15741388NEUTRON DIFFRACTION97
3.5101-4.41990.15331550.13561383NEUTRON DIFFRACTION97
4.4199-29.01230.1531620.14671419NEUTRON DIFFRACTION96

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