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- PDB-1ete: CRYSTAL STRUCTURE OF THE FLT3 LIGAND -

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Basic information

Entry
Database: PDB / ID: 1ete
TitleCRYSTAL STRUCTURE OF THE FLT3 LIGAND
ComponentsFLT3 LIGAND
KeywordsCYTOKINE / four-helix bundle
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 / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Fms-related tyrosine kinase 3 ligand
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsSavvides, S.N. / Boone, T. / Karplus, P.A.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Flt3 ligand structure and unexpected commonalities of helical bundles and cystine knots.
Authors: Savvides, S.N. / Boone, T. / Andrew Karplus, P.
History
DepositionApr 12, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FLT3 LIGAND
B: FLT3 LIGAND
C: FLT3 LIGAND
D: FLT3 LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,37213
Polymers61,7834
Non-polymers5899
Water3,855214
1
A: FLT3 LIGAND
B: FLT3 LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2848
Polymers30,8912
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-131 kcal/mol
Surface area13900 Å2
MethodPISA
2
C: FLT3 LIGAND
D: FLT3 LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0885
Polymers30,8912
Non-polymers1963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-93 kcal/mol
Surface area13330 Å2
MethodPISA
3
A: FLT3 LIGAND
B: FLT3 LIGAND
hetero molecules

C: FLT3 LIGAND
D: FLT3 LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,37213
Polymers61,7834
Non-polymers5899
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+1/2,y-1/2,-z1
Buried area4630 Å2
ΔGint-247 kcal/mol
Surface area26580 Å2
MethodPISA
4
A: FLT3 LIGAND
B: FLT3 LIGAND
hetero molecules

C: FLT3 LIGAND
D: FLT3 LIGAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,37213
Polymers61,7834
Non-polymers5899
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4630 Å2
ΔGint-239 kcal/mol
Surface area26580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.080, 159.410, 26.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
FLT3 LIGAND


Mass: 15445.717 Da / Num. of mol.: 4 / Fragment: RECEPTOR BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Bacteria (eubacteria) / References: UniProt: P49771
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsWATER 6049 WAS MODELED IN WHAT IS BELIEVED TO BE A LOW OCCUPANCY SITE FOR AN ORDERED ZINC ATOM.

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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: 2.32 Å3/Da / Density % sol: 46.98 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: PEG 8000, zinc acetate, sodium cacodylate, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: vapor diffusion
Details: drop consists of 1:1 mixture of well and protein solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110-15 mg/mlprotein1drop
220 mMHEPES1drop
31 mM EDTA1drop
46-9 %(w/v)PEG80001reservoir
50.2 Mzinc acetate1reservoir
60.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.92
DetectorType: PRINCETON 2K / Detector: CCD / Date: Jan 25, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 117033 / Num. obs: 29421 / % possible obs: 96.9 % / Observed criterion σ(I): 3.8 / Redundancy: 4 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 12
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.221 / Num. unique all: 1372 / % possible all: 95.5
Reflection shell
*PLUS
% possible obs: 95.5 % / Mean I/σ(I) obs: 3.8

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.851refinement
RefinementResolution: 2.2→20 Å / σ(F): 1 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.287 1471 RANDOM
Rwork0.239 --
all-29421 -
obs-28346 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4271 0 9 217 4497
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3

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