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- PDB-8ilx: mCherry-LaM3 complex -

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Basic information

Entry
Database: PDB / ID: 8ilx
TitlemCherry-LaM3 complex
Components
  • LAM3
  • MCherry fluorescent protein
KeywordsFLUORESCENT PROTEIN/IMMUNE SYSTEM / PROTEIN BINDING / FLUORESCENT PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green Fluorescent Protein / Green fluorescent protein / Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Immunoglobulins / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
MCherry fluorescent protein
Similarity search - Component
Biological speciesAnaplasma marginale (bacteria)
Camelus bactrianus (Bactrian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.29 Å
AuthorsLiang, H. / Liu, R. / Ding, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)32070939 China
National Science Foundation (NSF, China)82030106 China
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insights into the Binding of Red Fluorescent Protein mCherry-Specific Nanobodies.
Authors: Liang, H. / Ma, Z. / Wang, Z. / Zhong, P. / Li, R. / Jiang, H. / Zong, X. / Zhong, C. / Liu, X. / Liu, P. / Liu, J. / Zhu, H. / Liu, R. / Ding, Y.
History
DepositionMar 5, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MCherry fluorescent protein
B: MCherry fluorescent protein
C: LAM3
D: LAM3


Theoretical massNumber of molelcules
Total (without water)82,2004
Polymers82,2004
Non-polymers00
Water00
1
A: MCherry fluorescent protein
C: LAM3


Theoretical massNumber of molelcules
Total (without water)41,1002
Polymers41,1002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-9 kcal/mol
Surface area14170 Å2
MethodPISA
2
B: MCherry fluorescent protein
D: LAM3


Theoretical massNumber of molelcules
Total (without water)41,1002
Polymers41,1002
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-8 kcal/mol
Surface area14390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.867, 104.831, 68.508
Angle α, β, γ (deg.)90.00, 102.83, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MCherry fluorescent protein


Mass: 26797.229 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: CH6:MYG / Source: (gene. exp.) Anaplasma marginale (bacteria) / Gene: mCherry / Production host: Escherichia coli (E. coli) / References: UniProt: X5DSL3
#2: Antibody LAM3


Mass: 14302.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)
Has ligand of interestY
Has protein modificationY

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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: 2.87 Å3/Da / Density % sol: 57.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M sodium sulfate, 0.1 M Bis-Tris propane (pH 7.5), 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Sep 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.29→81.97 Å / Num. obs: 14166 / % possible obs: 99.9 % / Redundancy: 6.6 % / CC1/2: 0.818 / Rmerge(I) obs: 0.447 / Rpim(I) all: 0.199 / Rrim(I) all: 0.491 / Χ2: 0.88 / Net I/σ(I): 4.7 / Num. measured all: 93219
Reflection shellResolution: 3.29→3.38 Å / % possible obs: 100 % / Redundancy: 5.7 % / Rmerge(I) obs: 2.359 / Num. measured all: 5864 / Num. unique obs: 1033 / CC1/2: 0.346 / Rpim(I) all: 1.12 / Rrim(I) all: 2.619 / Χ2: 0.95 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
PDB_EXTRACT4data extraction
DIALSdata reduction
PHENIXphasing
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.29→66.8 Å / SU ML: 0.52 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 36.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3119 682 4.83 %
Rwork0.2638 --
obs0.2661 14108 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.29→66.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5074 0 0 0 5074
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.771
X-RAY DIFFRACTIONf_dihedral_angle_d6.995737
X-RAY DIFFRACTIONf_chiral_restr0.047759
X-RAY DIFFRACTIONf_plane_restr0.005917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.29-3.540.38331500.33372636X-RAY DIFFRACTION100
3.54-3.90.37231140.32412674X-RAY DIFFRACTION99
3.9-4.470.33051420.26952675X-RAY DIFFRACTION100
4.47-5.620.26411420.23172698X-RAY DIFFRACTION100
5.63-66.80.27091340.22512743X-RAY DIFFRACTION100

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