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- PDB-6bhp: Crystal structure of the Chlamydomonas reinhardtii LCI1 channel -

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Basic information

Entry
Database: PDB / ID: 6bhp
TitleCrystal structure of the Chlamydomonas reinhardtii LCI1 channel
ComponentsMembrane protein
KeywordsMEMBRANE PROTEIN / Channel / CO2-concentrating mechanism / microalgae
Function / homologymembrane / CARBON DIOXIDE / : / Membrane protein
Function and homology information
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.209 Å
AuthorsChou, T.-H. / Radhakrishnan, A.
CitationJournal: Plant J. / Year: 2020
Title: Structure and function of LCI1: a plasma membrane CO 2 channel in the Chlamydomonas CO 2 concentrating mechanism.
Authors: Kono, A. / Chou, T.H. / Radhakrishnan, A. / Bolla, J.R. / Sankar, K. / Shome, S. / Su, C.C. / Jernigan, R.L. / Robinson, C.V. / Yu, E.W. / Spalding, M.H.
History
DepositionOct 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Membrane protein
B: Membrane protein
C: Membrane protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2007
Polymers66,5543
Non-polymers6464
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-124 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.235, 85.235, 209.784
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Membrane protein


Mass: 22184.730 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q39583
#2: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO2

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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: 3.31 Å3/Da / Density % sol: 67.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5 / Details: PEG2000MME, sodium citrate, nickel chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15305 / % possible obs: 100 % / Redundancy: 9.4 % / Biso Wilson estimate: 43.3 Å2 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.044 / Rrim(I) all: 0.11 / Χ2: 0.899 / Net I/av σ(I): 20.5 / Net I/σ(I): 5.1 / Num. measured all: 143222
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)CC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
3.2-3.319.60.4710.5460.847100
3.31-3.459.70.650.3880.889100
3.45-3.69.60.8330.2630.8571000.7830.827
3.6-3.799.30.90.1840.9221000.5390.57
3.79-4.038.90.9430.1651.07599.90.4230.455
4.03-4.349.80.9840.0640.8581000.1930.203
4.34-4.789.50.990.0430.9261000.1280.135
4.78-5.4790.9910.0390.9261000.1130.12
5.47-6.899.60.9940.0310.8471000.0930.098
6.89-508.50.9990.0110.86499.90.030.032

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
SHELXCDphasing
HKL-2000data reduction
RefinementMethod to determine structure: SIRAS / Resolution: 3.209→42.753 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2968 617 4.93 %
Rwork0.2194 11910 -
obs0.2229 12527 82.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 126.11 Å2 / Biso mean: 25.9656 Å2 / Biso min: 3.52 Å2
Refinement stepCycle: final / Resolution: 3.209→42.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 6 0 4059
Biso mean--77.52 --
Num. residues----510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024156
X-RAY DIFFRACTIONf_angle_d0.5155662
X-RAY DIFFRACTIONf_chiral_restr0.039681
X-RAY DIFFRACTIONf_plane_restr0.003693
X-RAY DIFFRACTIONf_dihedral_angle_d13.9122403
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2086-3.53140.3462590.22011101116031
3.5314-4.0420.28281680.20963504367299
4.042-5.09120.27932160.202535393755100
5.0912-42.75730.31891740.241937663940100

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