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- PDB-5b60: Crystal structure of PtLCIB4 S47R mutant, a homolog of the limiti... -

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Basic information

Entry
Database: PDB / ID: 5b60
TitleCrystal structure of PtLCIB4 S47R mutant, a homolog of the limiting CO2-inducible protein LCIB
ComponentsPtLCIB4 S47R mutant
KeywordsMETAL BINDING PROTEIN / metalloenzyme
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
Function and homology information
Biological speciesPhaeodactylum tricornutum (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJin, S. / Sun, J. / Wunder, T. / Tang, D. / Mueller-Caja, 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 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: PtLCIB4 S47R mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4793
Polymers30,3781
Non-polymers1012
Water43224
1
A: PtLCIB4 S47R mutant
hetero molecules

A: PtLCIB4 S47R mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,9586
Polymers60,7562
Non-polymers2024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area2760 Å2
ΔGint-111 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.550, 66.110, 69.060
Angle α, β, γ (deg.)90.00, 101.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PtLCIB4 S47R mutant


Mass: 30377.990 Da / Num. of mol.: 1 / Mutation: S47R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phaeodactylum tricornutum (Diatom) / Production host: Escherichia coli (E. coli) / References: UniProt: B7FR29*PLUS
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence database of this protein is BAV00141 in GenBank. The residues (-12)-1 are N-terminal ...The sequence database of this protein is BAV00141 in GenBank. The residues (-12)-1 are N-terminal expression tags. This structure is S47R mutant.

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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: 51.35 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM sodium chloride, 100 mM Bis-Tris, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→67.8 Å / Num. obs: 15494 / % possible obs: 99.5 % / Redundancy: 8.8 % / Net I/σ(I): 11
Reflection shellResolution: 2.2→2.32 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALAdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5B5Y

5b5y


Resolution: 2.2→47.159 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.64 / Phase error: 27.48
RfactorNum. reflection% reflection
Rfree0.2537 770 5 %
Rwork0.2501 --
obs0.2503 15400 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.2→47.159 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1603 0 2 24 1629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121631
X-RAY DIFFRACTIONf_angle_d1.2722213
X-RAY DIFFRACTIONf_dihedral_angle_d14.082556
X-RAY DIFFRACTIONf_chiral_restr0.073258
X-RAY DIFFRACTIONf_plane_restr0.006287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2002-2.3380.32421320.34952419X-RAY DIFFRACTION100
2.338-2.51850.2761370.28142430X-RAY DIFFRACTION99
2.5185-2.7720.23411080.28562442X-RAY DIFFRACTION99
2.772-3.1730.31921400.28032434X-RAY DIFFRACTION99
3.173-3.99730.25511320.24072426X-RAY DIFFRACTION100
3.9973-47.16950.21911210.22282479X-RAY DIFFRACTION99

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