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- PDB-6ir1: Crystal structure of red fluorescent protein mCherry complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6ir1
TitleCrystal structure of red fluorescent protein mCherry complexed with the nanobody LaM4 at 1.9 Angstron resolution
Components
  • MCherry fluorescent protein
  • mCherry's nanobody LaM4
KeywordsFLUORESCENT PROTEIN / Complex / Nanobody / red fluorescent protein mCherry / LaM4
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 / Beta Barrel / 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: 1.919 Å
AuthorsDing, Y. / Wang, Z.Y. / Hu, R.T. / Chen, X.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)31470764 China
National Science Foundation (China)91527305 China
CitationJournal: Protein Sci. / Year: 2021
Title: Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry.
Authors: Wang, Z. / Li, L. / Hu, R. / Zhong, P. / Zhang, Y. / Cheng, S. / Jiang, H. / Liu, R. / Ding, Y.
History
DepositionNov 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _pdbx_validate_close_contact.auth_atom_id_2
Revision 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MCherry fluorescent protein
B: mCherry's nanobody LaM4


Theoretical massNumber of molelcules
Total (without water)40,8192
Polymers40,8192
Non-polymers00
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, 1:1, isothermal titration calorimetry, 1:1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-7 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.489, 41.665, 53.182
Angle α, β, γ (deg.)90.000, 90.630, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-225-

HOH

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Components

#1: Protein MCherry fluorescent protein


Mass: 26797.229 Da / Num. of mol.: 1
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: Antibody mCherry's nanobody LaM4


Mass: 14021.442 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Lithium sulfate monohydrate, 0.1M BIS-TRIS pH 5.5, 25%(w/v) Polyethylene glycol 3,350.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.919→40.26 Å / Num. obs: 24985 / % possible obs: 94.1 % / Redundancy: 6.4 % / Biso Wilson estimate: 25.2 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.07 / Rrim(I) all: 0.18 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.92-2.026.10.76937740.8190.3410.84398.2
6.07-40.266.50.148880.9760.0590.15299.1

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Q, 3K1K

2h5q

3k1k


Resolution: 1.919→32.554 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.39
RfactorNum. reflection% reflection
Rfree0.2319 1182 4.78 %
Rwork0.1799 --
obs0.1825 24709 92.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 150.2 Å2 / Biso mean: 35.3018 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 1.919→32.554 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2683 0 0 162 2845
Biso mean---37.31 -
Num. residues----341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132750
X-RAY DIFFRACTIONf_angle_d1.2563705
X-RAY DIFFRACTIONf_chiral_restr0.065379
X-RAY DIFFRACTIONf_plane_restr0.008483
X-RAY DIFFRACTIONf_dihedral_angle_d16.2181620
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9189-2.00620.29921460.25282889303592
2.0062-2.11190.3208830.25351808189157
2.1119-2.24420.30941530.20673111326499
2.2442-2.41740.26651440.193331633307100
2.4174-2.66060.26271430.19623128327199
2.6606-3.04540.2221640.18453092325698
3.0454-3.83590.21621810.165531413322100
3.8359-32.55870.19671680.15443195336398

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