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- PDB-7nbi: Crystal structure of a monomeric FLT3 Ligand variant -

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Basic information

Entry
Database: PDB / ID: 7nbi
TitleCrystal structure of a monomeric FLT3 Ligand variant
ComponentsFms-related tyrosine kinase 3 ligand
KeywordsDE NOVO PROTEIN / FLT3 Ligand / Engineered cytokine / monomeric FLT3 ligand
Function / homology
Function and homology information


dendritic cell differentiation / STAT5 Activation / FLT3 signaling through SRC family kinases / embryonic hemopoiesis / positive regulation of natural killer cell proliferation / PI3K Cascade / FLT3 signaling by CBL mutants / FLT3 Signaling / Negative regulation of FLT3 / B cell differentiation ...dendritic cell differentiation / STAT5 Activation / FLT3 signaling through SRC family kinases / embryonic hemopoiesis / positive regulation of natural killer cell proliferation / PI3K Cascade / FLT3 signaling by CBL mutants / FLT3 Signaling / Negative regulation of FLT3 / B cell differentiation / cytokine activity / receptor tyrosine kinase binding / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / signaling receptor binding / positive regulation of cell population proliferation / cell surface / signal transduction / extracellular space / extracellular region / membrane / plasma membrane / cytosol
Similarity search - Function
Flt3 ligand / flt3 ligand / Four-helical cytokine-like, core
Similarity search - Domain/homology
Fms-related tyrosine kinase 3 ligand
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsPannecoucke, E. / Raes, L. / Savvides, S.N.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Engineering and crystal structure of a monomeric FLT3 ligand variant.
Authors: Pannecoucke, E. / Raes, L. / Savvides, S.N.
History
DepositionJan 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fms-related tyrosine kinase 3 ligand
B: Fms-related tyrosine kinase 3 ligand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2317
Polymers31,7502
Non-polymers4805
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, size exclusion chromatography in line with multi-angle laser light scattering device
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-80 kcal/mol
Surface area13180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)28.300, 43.490, 46.360
Angle α, β, γ (deg.)82.820, 85.410, 85.100
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Fms-related tyrosine kinase 3 ligand / Flt3 ligand / Flt3L / SL cytokine


Mass: 15875.146 Da / Num. of mol.: 2 / Mutation: L33D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FLT3LG / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-gami B / References: UniProt: P49771
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.78 Å3/Da / Density % sol: 30.89 % / Description: Morphologically twinned
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 2.0 M ammonium sulfate, 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.65→18.64 Å / Num. obs: 70278 / % possible obs: 94.9 % / Redundancy: 8.81 % / Biso Wilson estimate: 16.9 Å2 / CC1/2: 0.996 / Rrim(I) all: 0.077 / Net I/σ(I): 10.6
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 2.37 % / Mean I/σ(I) obs: 2.33 / Num. unique obs: 4053 / CC1/2: 0.728 / Rrim(I) all: 0.567 / % possible all: 89.2

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Processing

Software
NameVersionClassification
XDSVERSION Jan 31, 2020data scaling
PHASERphasing
PHENIX1.19.1_4122refinement
BUSTER2.10.3refinement
XDSVERSION Jan 31, 2020data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ETE

1ete


Resolution: 1.65→18.42 Å / SU ML: 0.1961 / Cross valid method: FREE R-VALUE / Phase error: 22.5253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2026 1246 5 %
Rwork0.1643 23665 -
obs0.1662 24910 94.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.57 Å2
Refinement stepCycle: LAST / Resolution: 1.65→18.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2170 0 25 218 2413
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01752261
X-RAY DIFFRACTIONf_angle_d1.48973072
X-RAY DIFFRACTIONf_chiral_restr0.0896340
X-RAY DIFFRACTIONf_plane_restr0.0179397
X-RAY DIFFRACTIONf_dihedral_angle_d6.2138298
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.720.30781330.28762530X-RAY DIFFRACTION92.72
1.72-1.790.27691380.21522628X-RAY DIFFRACTION93.73
1.79-1.890.24331380.18182614X-RAY DIFFRACTION94.6
1.89-2.010.20241400.18012655X-RAY DIFFRACTION95.1
2.01-2.160.18481380.14572622X-RAY DIFFRACTION95.5
2.16-2.380.18361390.14492640X-RAY DIFFRACTION95.63
2.38-2.720.20151400.15632671X-RAY DIFFRACTION96.53
2.72-3.430.19811400.16042645X-RAY DIFFRACTION96.17
3.43-18.420.18661400.15392660X-RAY DIFFRACTION95.79
Refinement TLS params.Method: refined / Origin x: -9.80387887907 Å / Origin y: 34.3372772444 Å / Origin z: 52.6374430596 Å
111213212223313233
T0.0778154800444 Å2-0.00349774329364 Å2-0.00452947362204 Å2-0.0845710151639 Å20.00271611197028 Å2--0.0842227283259 Å2
L0.180380999753 °2-0.04513223838 °2-0.0613606161871 °2-0.174136085964 °2-0.0551592686399 °2--0.242403503501 °2
S-0.0222990504561 Å °-0.0126178183503 Å °-0.00494726007736 Å °-0.0119451884893 Å °-0.00525553695723 Å °0.00279873046016 Å °-0.0246820485145 Å °0.0127607374854 Å °-0.0245919055185 Å °
Refinement TLS groupSelection details: all

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