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- PDB-5b5x: Crystal structure of limiting CO2-inducible protein LCIC -

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Basic information

Entry
Database: PDB / ID: 5b5x
TitleCrystal structure of limiting CO2-inducible protein LCIC
Componentslimiting CO2-inducible protein LCIC
KeywordsMETAL BINDING PROTEIN / metalloprotein
Function / homologyLimiting CO2-inducible protein B/C, beta carbonyic anhydrase domain / Limiting CO2-inducible proteins B/C beta carbonyic anhydrases / metal ion binding / Low-CO2 inducible protein LCIC
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.511 Å
AuthorsJin, S. / Sun, J. / Wunder, T. / Tang, D. / Mueller-Cajar, O.M. / Gao, Y.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Singapore National Research FoundationNRF-RF2009-RF001-267 Singapore
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structural insights into the LCIB protein family reveals a new group of beta-carbonic anhydrases
Authors: Jin, S. / Sun, J. / Wunder, T. / Tang, D. / Cousins, A.B. / Sze, S.K. / Mueller-Cajar, O. / Gao, Y.G.
History
DepositionMay 24, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Mar 20, 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

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Assembly

Deposited unit
A: limiting CO2-inducible protein LCIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4163
Polymers33,2541
Non-polymers1612
Water25214
1
A: limiting CO2-inducible protein LCIC
hetero molecules

A: limiting CO2-inducible protein LCIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8316
Polymers66,5082
Non-polymers3234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+11
Buried area2990 Å2
ΔGint-131 kcal/mol
Surface area18710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.972, 88.004, 100.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein limiting CO2-inducible protein LCIC / Low-CO2 inducible protein LCIC / carbon dioxide concentrating mechanism related protein 2


Mass: 33254.035 Da / Num. of mol.: 1 / Fragment: UNP residues 40-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: LciC / Production host: Escherichia coli (E. coli) / References: UniProt: Q75NZ1
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 1.87 Å3/Da / Density % sol: 34.12 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 200 mM lithium sulfate monohydrate, 100 mM Bis-Tris, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 8828 / % possible obs: 98.3 % / Redundancy: 5.8 % / Net I/σ(I): 27.5
Reflection shellResolution: 2.5→2.54 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.511→34.469 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2826 409 4.74 %
Rwork0.2165 --
obs0.2195 8636 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.511→34.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1714 0 6 14 1734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091747
X-RAY DIFFRACTIONf_angle_d1.2462366
X-RAY DIFFRACTIONf_dihedral_angle_d14.05635
X-RAY DIFFRACTIONf_chiral_restr0.05279
X-RAY DIFFRACTIONf_plane_restr0.005302
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5109-2.87410.38851310.25412618X-RAY DIFFRACTION95
2.8741-3.62040.281390.22812766X-RAY DIFFRACTION100
3.6204-34.47240.25891390.20232843X-RAY DIFFRACTION98

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