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- PDB-6kfs: Structure of CCM related protein -

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Basic information

Entry
Database: PDB / ID: 6kfs
TitleStructure of CCM related protein
ComponentsLCIB_C_CA domain-containing protein
KeywordsMETAL BINDING PROTEIN / carbonic anhydrase / proton shuttle
Function / homologyLimiting CO2-inducible protein B/C, beta carbonyic anhydrase domain / Limiting CO2-inducible proteins B/C beta carbonyic anhydrases / metal ion binding / Limiting CO2-inducible protein B/C beta carbonyic anhydrase domain-containing protein / Limiting CO2-inducible protein B/C beta carbonyic anhydrase domain-containing protein
Function and homology information
Biological speciesPhaeodactylum tricornutum (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsJin, S. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (Singapore)MOE2015-T2-1-078 Singapore
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2020
Title: Structural and biochemical characterization of novel carbonic anhydrases from Phaeodactylum tricornutum.
Authors: Jin, S. / Vullo, D. / Bua, S. / Nocentini, A. / Supuran, C.T. / Gao, Y.G.
History
DepositionJul 8, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LCIB_C_CA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4632
Polymers28,3981
Non-polymers651
Water7,224401
1
A: LCIB_C_CA domain-containing protein
hetero molecules

A: LCIB_C_CA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9274
Polymers56,7962
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area4280 Å2
ΔGint-90 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.363, 93.363, 177.834
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-506-

HOH

21A-532-

HOH

31A-623-

HOH

41A-799-

HOH

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Components

#1: Protein LCIB_C_CA domain-containing protein


Mass: 28397.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylum tricornutum (Diatom) / Gene: pt43233 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A173LZ50, UniProt: B7FR28*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 401 / 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: 2.63 Å3/Da / Density % sol: 53.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M (NH4)SO4, 0.1M Bis-Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 93030 / % possible obs: 99.96 % / Redundancy: 22 % / Biso Wilson estimate: 13.37 Å2 / Net I/σ(I): 17.96
Reflection shellResolution: 1.2→1.23 Å / Num. unique obs: 6859

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→19.71 Å / SU ML: 0.135 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.9837
RfactorNum. reflection% reflection
Rfree0.1668 4678 5.03 %
Rwork0.1486 --
obs-93028 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 19.05 Å2
Refinement stepCycle: LAST / Resolution: 1.2→19.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1828 0 1 401 2230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00821874
X-RAY DIFFRACTIONf_angle_d0.97612541
X-RAY DIFFRACTIONf_chiral_restr0.078279
X-RAY DIFFRACTIONf_plane_restr0.0071343
X-RAY DIFFRACTIONf_dihedral_angle_d13.6955681
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.210.28011580.27542938X-RAY DIFFRACTION100
1.21-1.230.28441610.25392918X-RAY DIFFRACTION100
1.23-1.240.24611600.24972900X-RAY DIFFRACTION100
1.24-1.260.25471500.24252905X-RAY DIFFRACTION100
1.26-1.280.27781660.24662922X-RAY DIFFRACTION100
1.28-1.290.30321520.27312933X-RAY DIFFRACTION100
1.29-1.310.29251510.29762907X-RAY DIFFRACTION99.97
1.31-1.330.28661580.25762944X-RAY DIFFRACTION100
1.33-1.350.21031400.23852924X-RAY DIFFRACTION99.97
1.35-1.370.25741440.23362938X-RAY DIFFRACTION100
1.37-1.40.2641550.222909X-RAY DIFFRACTION100
1.4-1.420.22561420.21582949X-RAY DIFFRACTION100
1.42-1.450.21971620.2182917X-RAY DIFFRACTION100
1.45-1.480.1891560.20512936X-RAY DIFFRACTION100
1.48-1.510.23051580.20342938X-RAY DIFFRACTION100
1.51-1.550.21141520.20142922X-RAY DIFFRACTION100
1.55-1.590.23171560.19912941X-RAY DIFFRACTION100
1.59-1.630.21641720.19692920X-RAY DIFFRACTION100
1.63-1.680.19521760.19092904X-RAY DIFFRACTION100
1.68-1.730.22091570.19472943X-RAY DIFFRACTION100
1.73-1.790.17871420.18882959X-RAY DIFFRACTION100
1.79-1.860.18041350.18462994X-RAY DIFFRACTION100
1.86-1.950.19031370.17372946X-RAY DIFFRACTION100
1.95-2.050.16431520.16962955X-RAY DIFFRACTION100
2.05-2.180.1831770.16172935X-RAY DIFFRACTION100
2.18-2.350.17071640.15612959X-RAY DIFFRACTION100
2.35-2.580.19481440.15882994X-RAY DIFFRACTION100
2.58-2.960.18491640.15692985X-RAY DIFFRACTION100
2.96-3.720.17481600.14453008X-RAY DIFFRACTION99.97
3.72-19.710.17621770.15433107X-RAY DIFFRACTION100

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