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- PDB-8im1: mCherry-LaM1 complex -

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Basic information

Entry
Database: PDB / ID: 8im1
TitlemCherry-LaM1 complex
Components
  • LaM1
  • 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: 2.05 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 23, 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: LaM1
C: MCherry fluorescent protein
D: LaM1
E: MCherry fluorescent protein
F: LaM1
G: MCherry fluorescent protein
H: LaM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,52818
Polymers163,5688
Non-polymers96110
Water9,494527
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.070, 74.830, 94.640
Angle α, β, γ (deg.)111.33, 100.68, 104.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
MCherry fluorescent protein


Mass: 26797.229 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaplasma marginale (bacteria) / Gene: mCherry / Production host: Escherichia coli (E. coli) / References: UniProt: X5DSL3
#2: Protein
LaM1


Mass: 14094.711 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M Potassium sulfate, 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: 2.05→41.97 Å / Num. obs: 97591 / % possible obs: 96.9 % / Redundancy: 3.6 % / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.053 / Rrim(I) all: 0.101 / Χ2: 0.84 / Net I/σ(I): 9 / Num. measured all: 349365
Reflection shellResolution: 2.05→2.1 Å / % possible obs: 96 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.987 / Num. measured all: 25139 / Num. unique obs: 7164 / CC1/2: 0.54 / Rpim(I) all: 0.619 / Rrim(I) all: 1.169 / Χ2: 0.81 / Net I/σ(I) obs: 1.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
Aimlessdata scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→32.13 Å / SU ML: 0.29 / Cross valid method: NONE / σ(F): 1.97 / Phase error: 29.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 4723 4.84 %
Rwork0.2045 --
obs0.206 97559 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→32.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10492 0 50 527 11069
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002
X-RAY DIFFRACTIONf_angle_d0.691
X-RAY DIFFRACTIONf_dihedral_angle_d7.0721486
X-RAY DIFFRACTIONf_chiral_restr0.0451525
X-RAY DIFFRACTIONf_plane_restr0.0041878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.070.35821470.35283138X-RAY DIFFRACTION96
2.07-2.10.35341640.33273002X-RAY DIFFRACTION96
2.1-2.120.38031370.3313152X-RAY DIFFRACTION97
2.12-2.150.35241690.32523057X-RAY DIFFRACTION96
2.15-2.180.33441850.30183039X-RAY DIFFRACTION97
2.18-2.210.3441490.28413157X-RAY DIFFRACTION97
2.21-2.240.3421740.28253021X-RAY DIFFRACTION97
2.24-2.270.3091570.27223126X-RAY DIFFRACTION97
2.27-2.310.26791810.25943113X-RAY DIFFRACTION97
2.31-2.350.29711470.26273096X-RAY DIFFRACTION98
2.35-2.390.2971500.25663083X-RAY DIFFRACTION97
2.39-2.430.3291620.25893158X-RAY DIFFRACTION97
2.43-2.480.29271530.25433070X-RAY DIFFRACTION98
2.48-2.530.30331520.25383138X-RAY DIFFRACTION98
2.53-2.580.29681650.26163143X-RAY DIFFRACTION98
2.58-2.640.32061680.25023112X-RAY DIFFRACTION98
2.64-2.710.27741360.24553106X-RAY DIFFRACTION98
2.71-2.780.32191870.24423098X-RAY DIFFRACTION98
2.78-2.860.27361490.24313148X-RAY DIFFRACTION98
2.86-2.960.25651570.23083119X-RAY DIFFRACTION98
2.96-3.060.28031420.22493122X-RAY DIFFRACTION98
3.06-3.180.2551440.22213114X-RAY DIFFRACTION98
3.18-3.330.26641430.2093142X-RAY DIFFRACTION98
3.33-3.50.20721650.18873136X-RAY DIFFRACTION98
3.5-3.720.22791600.18543094X-RAY DIFFRACTION97
3.72-4.010.20421850.17783048X-RAY DIFFRACTION96
4.01-4.410.18611450.15013079X-RAY DIFFRACTION96
4.41-5.050.15241510.13953049X-RAY DIFFRACTION95
5.05-6.350.16741510.1643033X-RAY DIFFRACTION95
6.35-32.130.19191480.18212943X-RAY DIFFRACTION92

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