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- PDB-7c5y: Crystal structure of the iota-carbonic anhydrase from eukaryotic ... -

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Basic information

Entry
Database: PDB / ID: 7c5y
TitleCrystal structure of the iota-carbonic anhydrase from eukaryotic microalga complexed with iodide
Componentsiota-carbonic anhydrase
KeywordsLYASE / carbonic anhydrase / iodide complex
Function / homologyNuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / IODIDE ION
Function and homology information
Biological speciesBigelowiella natans (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSenda, M. / Senda, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP17am0101001 Japan
CitationJournal: Bmc Biol. / Year: 2021
Title: Characterization of a novel type of carbonic anhydrase that acts without metal cofactors.
Authors: Hirakawa, Y. / Senda, M. / Fukuda, K. / Yu, H.Y. / Ishida, M. / Taira, M. / Kinbara, K. / Senda, T.
History
DepositionMay 20, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iota-carbonic anhydrase
B: iota-carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,6108
Polymers110,8482
Non-polymers7616
Water10,467581
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9950 Å2
ΔGint-67 kcal/mol
Surface area40770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.781, 192.898, 58.206
Angle α, β, γ (deg.)90.000, 96.459, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein iota-carbonic anhydrase


Mass: 55424.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bigelowiella natans (eukaryote) / Production host: Escherichia coli (E. coli) / References: carbonic anhydrase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 581 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 20%(w/v) PEG4000, 20%(v/v) i-propanol, 0.1 M sodium citrate pH 5.6

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.2→49.6 Å / Num. obs: 101667 / % possible obs: 99 % / Redundancy: 7 % / Biso Wilson estimate: 20.31 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.56
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 7 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.17 / Num. unique obs: 14779

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MR native SAD phasing using 7C5W as a partial model

7c5w


Resolution: 2.2→49.6 Å / SU ML: 0.2117 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.7267
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 5080 5 %
Rwork0.1667 96570 -
obs0.1688 101650 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.73 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7538 0 6 581 8125
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717733
X-RAY DIFFRACTIONf_angle_d0.756210511
X-RAY DIFFRACTIONf_chiral_restr0.0521103
X-RAY DIFFRACTIONf_plane_restr0.00521396
X-RAY DIFFRACTIONf_dihedral_angle_d7.85821078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.2371680.17683174X-RAY DIFFRACTION95.81
2.23-2.250.24511660.17553155X-RAY DIFFRACTION97.62
2.25-2.280.23831660.18353120X-RAY DIFFRACTION97.25
2.28-2.310.22511670.18563215X-RAY DIFFRACTION98.11
2.31-2.340.22771680.17693219X-RAY DIFFRACTION97.33
2.34-2.370.24471670.17823166X-RAY DIFFRACTION98.26
2.37-2.40.24881630.19363115X-RAY DIFFRACTION98.47
2.4-2.440.27781730.18313275X-RAY DIFFRACTION98.01
2.44-2.480.20721670.17973161X-RAY DIFFRACTION98.32
2.48-2.520.23021720.18323242X-RAY DIFFRACTION98.67
2.52-2.560.27371660.18453143X-RAY DIFFRACTION98.57
2.56-2.610.20661750.17843298X-RAY DIFFRACTION98.78
2.61-2.660.23281650.17293133X-RAY DIFFRACTION99.22
2.66-2.710.2381730.17563280X-RAY DIFFRACTION99.02
2.71-2.770.22821700.17423241X-RAY DIFFRACTION99.33
2.77-2.840.21551660.16833168X-RAY DIFFRACTION99.34
2.84-2.910.25891740.17193322X-RAY DIFFRACTION99.52
2.91-2.990.26151650.17043134X-RAY DIFFRACTION99.64
2.99-3.070.19071720.16683296X-RAY DIFFRACTION99.66
3.07-3.170.22971700.16873208X-RAY DIFFRACTION99.7
3.17-3.290.191720.17883222X-RAY DIFFRACTION99.85
3.29-3.420.19891720.16333305X-RAY DIFFRACTION99.97
3.42-3.570.18251720.15963255X-RAY DIFFRACTION100
3.57-3.760.19631670.15213199X-RAY DIFFRACTION100
3.76-40.1771720.14523260X-RAY DIFFRACTION100
4-4.30.17061720.13883273X-RAY DIFFRACTION100
4.31-4.740.18911700.1433254X-RAY DIFFRACTION99.97
4.74-5.420.17241710.15633246X-RAY DIFFRACTION100
5.42-6.830.2281710.19783250X-RAY DIFFRACTION99.94
6.83-49.60.14651680.16943241X-RAY DIFFRACTION99.5

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