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- PDB-6ir2: Crystal structure of red fluorescent protein mCherry complexed wi... -

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Basic information

Entry
Database: PDB / ID: 6ir2
TitleCrystal structure of red fluorescent protein mCherry complexed with the nanobody LaM2 at 1.4 Angstron resolution
Components
  • MCherry fluorescent protein
  • mCherry's nanobody LaM2
KeywordsFLUORESCENT PROTEIN / Complex / Nanobody / red fluorescent protein mCherry / LaM2
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: 1.393 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 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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's nanobody LaM2


Theoretical massNumber of molelcules
Total (without water)39,5202
Polymers39,5202
Non-polymers00
Water9,566531
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, 1:1, isothermal titration calorimetry, 1:1
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-5 kcal/mol
Surface area14930 Å2
Unit cell
Length a, b, c (Å)49.817, 61.046, 109.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MCherry fluorescent protein


Mass: 25714.033 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 LaM2


Mass: 13806.167 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.: 531 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2M Magnesium chloride hexahydrate, 0.1M Tris pH 8.5, 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: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.393→30 Å / Num. obs: 65784 / % possible obs: 97.9 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.043 / Rrim(I) all: 0.145 / Χ2: 2.585 / Net I/σ(I): 7.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.4-1.458.21.50464070.6620.5321.5991.05197
1.45-1.5110.21.20865000.7670.3851.271.10997.9
1.51-1.5811.30.91765360.8620.2780.9591.20398.5
1.58-1.6612.30.6765780.9230.1950.6991.3999
1.66-1.7612.40.45866480.9560.1330.4781.64799.6
1.76-1.911.70.30366140.9740.0920.3172.23599.4
1.9-2.0912.10.21567160.9840.0650.2253.40199.8
2.09-2.3910.80.14563120.9850.0460.1533.73593.7
2.39-3.0212.30.10367950.9950.0310.1084.394100
3.02-3010.70.07466780.9970.0230.0785.14594.4

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H5Q,3K1K

2h5q

3k1k


Resolution: 1.393→29.396 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.47
RfactorNum. reflection% reflection
Rfree0.2158 3196 4.87 %
Rwork0.195 --
obs0.1961 65647 97.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.38 Å2 / Biso mean: 20.2168 Å2 / Biso min: 8.38 Å2
Refinement stepCycle: final / Resolution: 1.393→29.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 0 531 3219
Biso mean---30.48 -
Num. residues----339
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062759
X-RAY DIFFRACTIONf_angle_d1.0263718
X-RAY DIFFRACTIONf_chiral_restr0.099379
X-RAY DIFFRACTIONf_plane_restr0.005481
X-RAY DIFFRACTIONf_dihedral_angle_d11.4581442
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3934-1.41420.31891410.26992439258090
1.4142-1.43630.25351340.26812685281997
1.4363-1.45980.2831430.25232693283697
1.4598-1.4850.26381200.24852675279598
1.485-1.5120.28091250.23452737286299
1.512-1.54110.27221310.22782697282898
1.5411-1.57250.23191270.22652731285898
1.5725-1.60670.26031510.21652726287799
1.6067-1.64410.23361250.212427402865100
1.6441-1.68520.25431440.206627252869100
1.6852-1.73080.24851640.206327272891100
1.7308-1.78170.21661540.202527642918100
1.7817-1.83920.26211530.207327512904100
1.8392-1.90490.23791380.21232721285999
1.9049-1.98110.26681450.23372734287999
1.9811-2.07130.18641320.186427962928100
2.0713-2.18050.19281480.185727682916100
2.1805-2.3170.27341200.21222399251985
2.317-2.49580.23741420.198128052947100
2.4958-2.74680.2091350.199528122947100
2.7468-3.14390.19181520.188628392991100
3.1439-3.95950.18051090.16142495260487
3.9595-29.4030.17511630.165429923155100

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