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- PDB-7saj: Crystal Structure of LaM2 Nanobody bound to mCherry -

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Basic information

Entry
Database: PDB / ID: 7saj
TitleCrystal Structure of LaM2 Nanobody bound to mCherry
Components
  • mCherry
  • nanobody LaM2
KeywordsIMMUNE SYSTEM / Antibody / nanobody / affinity tag / fluorescent protein
Function / homology
Function and homology information


bioluminescence / generation of precursor metabolites and energy
Similarity search - Function
Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesDiscosoma sp. (sea anemone)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsCong, A.T.Q. / Schellenberg, M.J.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Protein Sci. / Year: 2022
Title: High-efficiency recombinant protein purification using mCherry and YFP nanobody affinity matrices.
Authors: Cong, A.T.Q. / Witter, T.L. / Schellenberg, M.J.
History
DepositionSep 22, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mCherry
B: nanobody LaM2
C: mCherry
D: nanobody LaM2
E: mCherry
F: nanobody LaM2
G: mCherry
H: nanobody LaM2
I: mCherry
J: nanobody LaM2


Theoretical massNumber of molelcules
Total (without water)204,23310
Polymers204,23310
Non-polymers00
Water3,297183
1
A: mCherry
B: nanobody LaM2


Theoretical massNumber of molelcules
Total (without water)40,8472
Polymers40,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: mCherry
D: nanobody LaM2


Theoretical massNumber of molelcules
Total (without water)40,8472
Polymers40,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: mCherry
F: nanobody LaM2


Theoretical massNumber of molelcules
Total (without water)40,8472
Polymers40,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: mCherry
H: nanobody LaM2


Theoretical massNumber of molelcules
Total (without water)40,8472
Polymers40,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: mCherry
J: nanobody LaM2


Theoretical massNumber of molelcules
Total (without water)40,8472
Polymers40,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)171.437, 160.560, 88.786
Angle α, β, γ (deg.)90.000, 109.020, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
31chain E
41chain G
51chain I
12chain B
22chain D
32chain F
42chain H
52chain J

NCS domain segments:

Component-ID: 1 / End auth comp-ID: SER / End label comp-ID: SER

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETchain AAA5 - 22213 - 228
21METMETchain CCC5 - 22213 - 228
31METMETchain EEE5 - 22213 - 228
41METMETchain GGG5 - 22213 - 228
51METMETchain III5 - 22213 - 228
12VALVALchain BBB16 - 1394 - 127
22VALVALchain DDD16 - 1394 - 127
32VALVALchain FFF16 - 1394 - 127
42VALVALchain HHH16 - 1394 - 127
52VALVALchain JJJ16 - 1394 - 127

NCS ensembles :
ID
1
2

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Components

#1: Protein
mCherry


Mass: 26996.393 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Discosoma sp. (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A366VY15
#2: Antibody
nanobody LaM2


Mass: 13850.285 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.71 Å3/Da / Density % sol: 54.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.5M malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 29, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.25→71 Å / Num. obs: 106342 / % possible obs: 99.1 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.039 / Rrim(I) all: 0.074 / Χ2: 1.002 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.25-2.333.60.864106730.5250.5341.0190.98499.5
2.33-2.423.50.653105690.7050.4070.7730.99799.3
2.42-2.533.30.473103440.7960.30.5631.02996.3
2.53-2.673.70.358106450.8820.2170.421.03799.5
2.67-2.833.70.228106390.9550.1380.2671.04399.8
2.83-3.053.70.142107010.9790.0860.1671.03199.8
3.05-3.363.60.076106860.9940.0460.0890.9999.5
3.36-3.853.40.046105480.9970.0290.0540.93798.3
3.85-4.853.80.032107560.9990.0190.0370.951100
4.85-503.60.025107810.9990.0150.031.01699.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2h5q

2h5q


Resolution: 2.37→71 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2341 1589 1.74 %
Rwork0.2076 89625 -
obs0.2081 91214 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.02 Å2 / Biso mean: 79.1832 Å2 / Biso min: 39.19 Å2
Refinement stepCycle: final / Resolution: 2.37→71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13470 0 0 183 13653
Biso mean---60.49 -
Num. residues----1700
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5457X-RAY DIFFRACTION11.533TORSIONAL
12C5457X-RAY DIFFRACTION11.533TORSIONAL
13E5457X-RAY DIFFRACTION11.533TORSIONAL
14G5457X-RAY DIFFRACTION11.533TORSIONAL
15I5457X-RAY DIFFRACTION11.533TORSIONAL
21B2845X-RAY DIFFRACTION11.533TORSIONAL
22D2845X-RAY DIFFRACTION11.533TORSIONAL
23F2845X-RAY DIFFRACTION11.533TORSIONAL
24H2845X-RAY DIFFRACTION11.533TORSIONAL
25J2845X-RAY DIFFRACTION11.533TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.37-2.440.34141440.31678059820398
2.44-2.530.33281380.31077905804397
2.53-2.630.31071450.29948193833899
2.63-2.750.32231450.281781768321100
2.75-2.90.32731460.264181788324100
2.9-3.080.25521450.271382398384100
3.08-3.320.29611460.236581748320100
3.32-3.650.22211430.20458113825699
3.65-4.180.20831440.18538195833999
4.18-5.260.16821450.15328161830699
5.27-710.23191480.19368232838099
Refinement TLS params.Method: refined / Origin x: -46.919 Å / Origin y: 63.0757 Å / Origin z: 12.0023 Å
111213212223313233
T0.5405 Å20.1122 Å2-0.0315 Å2-0.4474 Å20.0213 Å2--0.542 Å2
L0.322 °2-0.1253 °20.0397 °2-0.2065 °20.0503 °2---0.0912 °2
S0.002 Å °0.0172 Å °0.0048 Å °-0.0828 Å °0.0037 Å °0.0168 Å °-0.0253 Å °-0.0377 Å °-0.0099 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA5 - 222
2X-RAY DIFFRACTION1allB16 - 139
3X-RAY DIFFRACTION1allC5 - 222
4X-RAY DIFFRACTION1allD16 - 139
5X-RAY DIFFRACTION1allE5 - 222
6X-RAY DIFFRACTION1allF16 - 139
7X-RAY DIFFRACTION1allG5 - 222
8X-RAY DIFFRACTION1allH16 - 139
9X-RAY DIFFRACTION1allI5 - 222
10X-RAY DIFFRACTION1allJ16 - 139
11X-RAY DIFFRACTION1allS1 - 207

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