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- PDB-5dxw: Crystal structure of mouse PD-L1 nanobody -

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Basic information

Entry
Database: PDB / ID: 5dxw
TitleCrystal structure of mouse PD-L1 nanobody
ComponentsPD-L1 nanobody
KeywordsSIGNALING PROTEIN / IG FOLD
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesCamelidae (mammal)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.441 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Samanta, D. / Almo, S.C. / Ploegh, H. / Ingram, J. / Dougan, M.
CitationJournal: To Be Published
Title: Crystal structure of mouse PD-L1 nanobody
Authors: Fedorov, A.A. / Fedorov, E.V. / Samanta, D. / Almo, S.C.
History
DepositionSep 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Structure summary
Revision 1.2Jan 30, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_struct_oper_list / struct_keywords
Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 23, 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: PD-L1 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5353
Polymers14,3431
Non-polymers1922
Water1,63991
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-25 kcal/mol
Surface area6150 Å2
MethodPISA
3
A: PD-L1 nanobody
hetero molecules

A: PD-L1 nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0706
Polymers28,6862
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area2430 Å2
ΔGint-77 kcal/mol
Surface area10530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.191, 29.679, 35.268
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-201-

SO4

21A-350-

HOH

31A-378-

HOH

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Components

#1: Antibody PD-L1 nanobody


Mass: 14342.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae (mammal) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 1.76 Å3/Da / Density % sol: 30.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 400, ammonium sulfate, hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 11, 2015
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.441→18.23 Å / Num. obs: 30989 / % possible obs: 99.31 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Net I/σ(I): 23.4

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Processing

Software
NameVersionClassification
PHENIX1.8_1069refinement
CBASSdata collection
HKL-2000data reduction
PHASERphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OL0

1ol0


Resolution: 1.441→18.23 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 21.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1934 689 4.08 %Random
Rwork0.1686 ---
obs0.1695 30989 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.441→18.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms885 0 10 91 986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006940
X-RAY DIFFRACTIONf_angle_d1.0671277
X-RAY DIFFRACTIONf_dihedral_angle_d12.018342
X-RAY DIFFRACTIONf_chiral_restr0.076137
X-RAY DIFFRACTIONf_plane_restr0.005166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.441-1.49860.31921530.31263118X-RAY DIFFRACTION95
1.4986-1.56680.30341420.2663327X-RAY DIFFRACTION100
1.5668-1.64930.24831600.21383319X-RAY DIFFRACTION100
1.6493-1.75260.22611440.19683307X-RAY DIFFRACTION100
1.7526-1.88780.22781340.17323309X-RAY DIFFRACTION100
1.8878-2.07750.17671540.15723334X-RAY DIFFRACTION100
2.0775-2.37760.21861250.15293335X-RAY DIFFRACTION100
2.3776-2.99330.20431230.16073353X-RAY DIFFRACTION100
2.9933-18.23280.13231300.13853322X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 73.9732 Å / Origin y: 1.2282 Å / Origin z: 31.1489 Å
111213212223313233
T0.0223 Å20.0042 Å2-0.005 Å2-0.0513 Å20.0012 Å2--0.0535 Å2
L1.3893 °20.0252 °2-0.4295 °2-1.2578 °2-0.2341 °2--2.1791 °2
S0.0285 Å °0.0035 Å °0.0316 Å °-0.0046 Å °0.0207 Å °-0.0376 Å °-0.0428 Å °-0.0399 Å °-0.0384 Å °
Refinement TLS groupSelection details: chain A

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