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

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Basic information

Entry
Database: PDB / ID: 6fji
TitleJoint neutron and x-ray crystal structure of human carbonic anhydrase IX mimic (apo).
ComponentsCarbonic anhydrase 2
KeywordsLYASE / joint X-ray neutron diffraction / 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
DEUTERATED WATER / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / NEUTRON DIFFRACTION / NUCLEAR REACTOR / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsFisher, S.Z.
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
DepositionJan 22, 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)29,2662
Polymers29,2011
Non-polymers651
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23620 Å2
ΔGint-11 kcal/mol
Surface area12070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.480, 41.850, 72.831
Angle α, β, γ (deg.)90.00, 104.07, 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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / 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-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 1.2 M sodium citrate 100 mM Tris pH 8.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12931
22931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
NUCLEAR REACTORILL LADI III12.8 - 4.0
SYNCHROTRONMAX II I911-221.04
Detector
TypeIDDetectorDate
LADI III1IMAGE PLATEDec 1, 2015
MAR CCD 130 mm2CCDOct 28, 2014
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LAUELneutron1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
12.81
241
31.041
Reflection

Entry-ID: 6FJI

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsDiffraction-IDNet I/σ(I)Rrim(I) all
2-401176373.64.20.13718.5
1.6-293178196.12.8217.80.05
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-IDRrim(I) all
2-2.110.051
1.6-1.720.24

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
LAUEGENdata reduction
SCALEPACKdata scaling
Refinement

SU ML: 0.14 / Cross valid method: THROUGHOUT / Method to determine structure: MOLECULAR REPLACEMENT / Phase error: 14.94 / Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Starting model: 4riv

4riv

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDσ(F)
1.6-26.993X-RAY DIFFRACTION0.16130.12970.13131585317664.9996.1721.36
2.033-28.949NEUTRON DIFFRACTION0.22160.18540.1872582117564.9572.491
Refinement stepCycle: LAST / Resolution: 1.6→26.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2052 0 1 199 2252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0155074
X-RAY DIFFRACTIONf_angle_d1.3728705
X-RAY DIFFRACTIONf_dihedral_angle_d20.9481326
X-RAY DIFFRACTIONf_chiral_restr0.122317
X-RAY DIFFRACTIONf_plane_restr0.006950
NEUTRON DIFFRACTIONf_bond_d0.0155074
NEUTRON DIFFRACTIONf_angle_d1.3728705
NEUTRON DIFFRACTIONf_dihedral_angle_d20.9481326
NEUTRON DIFFRACTIONf_chiral_restr0.122317
NEUTRON DIFFRACTIONf_plane_restr0.006950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.65160.21581390.17892679X-RAY DIFFRACTION94
1.6516-1.71070.21681480.1592682X-RAY DIFFRACTION95
1.7107-1.77910.19391480.1482705X-RAY DIFFRACTION96
1.7791-1.86010.15661410.142729X-RAY DIFFRACTION96
1.8601-1.95810.16831380.13392700X-RAY DIFFRACTION96
1.9581-2.08080.18531450.1312764X-RAY DIFFRACTION97
2.0808-2.24140.15981540.13152718X-RAY DIFFRACTION96
2.2414-2.46680.17681400.13212786X-RAY DIFFRACTION97
2.4668-2.82340.15961360.13742779X-RAY DIFFRACTION97
2.8234-3.55590.171500.12842807X-RAY DIFFRACTION98
3.5559-26.99710.11811460.10562832X-RAY DIFFRACTION96
2.0328-2.23730.27171220.23122164NEUTRON DIFFRACTION57
2.2373-2.56080.2381170.20122531NEUTRON DIFFRACTION66
2.5608-3.22570.22711540.19632906NEUTRON DIFFRACTION75
3.2257-28.95180.19941890.16183573NEUTRON DIFFRACTION91

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