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- PDB-7c5v: Crystal structure of the iota-carbonic anhydrase from cyanobacter... -

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Basic information

Entry
Database: PDB / ID: 7c5v
TitleCrystal structure of the iota-carbonic anhydrase from cyanobacterium complexed with bicarbonate
Componentsiota-carbonic anhydrase
KeywordsLYASE / carbonic anhydrase / bicarbonate complex
Function / homologyUncharacterised conserved protein UCP028288 / NTF2-like domain superfamily / carbonic anhydrase / lyase activity / BICARBONATE ION / Metal-independent carbonic anhydrase
Function and homology information
Biological speciesNostoc sp. PCC 7120 = FACHB-418 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 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)38,7384
Polymers38,6162
Non-polymers1222
Water905
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)77,4758
Polymers77,2314
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10920 Å2
ΔGint-91 kcal/mol
Surface area23890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.841, 83.734, 87.267
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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
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-1A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Dec 2, 2019
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.65→45.2 Å / Num. obs: 21732 / % possible obs: 100 % / Redundancy: 7 % / Biso Wilson estimate: 60.84 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.49
Reflection shellResolution: 2.65→2.79 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 3090 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18_3845refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C5W

7c5w


Resolution: 2.65→45.2 Å / SU ML: 0.3073 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.5362
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2631 1083 4.99 %
Rwork0.2071 20639 -
obs0.2099 21722 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.79 Å2
Refinement stepCycle: LAST / Resolution: 2.65→45.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2401 0 8 5 2414
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00732461
X-RAY DIFFRACTIONf_angle_d0.91663368
X-RAY DIFFRACTIONf_chiral_restr0.0502398
X-RAY DIFFRACTIONf_plane_restr0.0049435
X-RAY DIFFRACTIONf_dihedral_angle_d14.8558346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.770.33051380.27792574X-RAY DIFFRACTION100
2.77-2.920.29111330.25222606X-RAY DIFFRACTION99.89
2.92-3.10.45241330.28962581X-RAY DIFFRACTION99.96
3.1-3.340.34061340.23622555X-RAY DIFFRACTION100
3.34-3.670.29651350.23312581X-RAY DIFFRACTION99.96
3.67-4.210.24041410.18652571X-RAY DIFFRACTION100
4.21-5.30.19141400.16492590X-RAY DIFFRACTION100
5.3-45.20.24751290.19362581X-RAY DIFFRACTION99.74

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