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- PDB-7c5w: Crystal structure of the iota-carbonic anhydrase from cyanobacter... -

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Basic information

Entry
Database: PDB / ID: 7c5w
TitleCrystal structure of the iota-carbonic anhydrase from cyanobacterium complexed with iodide
Componentsiota-carbonic anhydrase
KeywordsLYASE / carbonic anhydrase / iodide complex
Function / homology
Function and homology information


carbonic anhydrase / lyase activity
Similarity search - Function
Uncharacterised conserved protein UCP028288 / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Metal-independent carbonic anhydrase
Similarity search - Component
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 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 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)38,8704
Polymers38,6162
Non-polymers2542
Water21612
1
A: iota-carbonic anhydrase
B: iota-carbonic anhydrase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)77,7398
Polymers77,2314
Non-polymers5084
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10900 Å2
ΔGint-100 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.519, 83.006, 88.136
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein iota-carbonic anhydrase


Mass: 19307.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. PCC 7120 = FACHB-418 (bacteria)
Strain: PCC 7120 / Gene: all2909 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8YT18
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.53 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 2.4 M sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 25, 2019
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.3→45.75 Å / Num. obs: 33691 / % possible obs: 99.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 55.49 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.18
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.9 / Num. unique obs: 4738 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
XSCALEdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→45.75 Å / SU ML: 0.3238 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 32.6286
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2438 1677 4.98 %
Rwork0.2214 31992 -
obs0.2226 33669 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 64.12 Å2
Refinement stepCycle: LAST / Resolution: 2.3→45.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2411 0 2 12 2425
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01342465
X-RAY DIFFRACTIONf_angle_d1.68833372
X-RAY DIFFRACTIONf_chiral_restr0.0902399
X-RAY DIFFRACTIONf_plane_restr0.0053432
X-RAY DIFFRACTIONf_dihedral_angle_d17.4907820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.370.38291380.36352639X-RAY DIFFRACTION99
2.37-2.440.34971390.33232664X-RAY DIFFRACTION99.86
2.44-2.530.38131400.31182669X-RAY DIFFRACTION99.93
2.53-2.630.39841440.29942638X-RAY DIFFRACTION99.93
2.63-2.750.34461430.27512692X-RAY DIFFRACTION99.93
2.75-2.90.311350.25182634X-RAY DIFFRACTION99.93
2.9-3.080.26841430.27332701X-RAY DIFFRACTION99.93
3.08-3.320.32381370.2492674X-RAY DIFFRACTION100
3.32-3.650.28621410.24552653X-RAY DIFFRACTION100
3.65-4.180.2491400.20622670X-RAY DIFFRACTION100
4.18-5.260.14731400.16652684X-RAY DIFFRACTION100
5.26-45.750.1911370.18592674X-RAY DIFFRACTION100

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