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- PDB-1scf: HUMAN RECOMBINANT STEM CELL FACTOR -

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Basic information

Entry
Database: PDB / ID: 1scf
TitleHUMAN RECOMBINANT STEM CELL FACTOR
ComponentsSTEM CELL FACTOR
KeywordsHORMONE/GROWTH FACTOR / HUMAN STEM CELL FACTOR / STEEL FACTOR / KIT LIGAND / MAST CELL GROWTH FACTOR / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


positive regulation of myeloid leukocyte differentiation / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic stem cell proliferation / positive regulation of hematopoietic progenitor cell differentiation / negative regulation of mast cell apoptotic process / melanocyte migration / positive regulation of melanocyte differentiation / myeloid leukocyte differentiation / positive regulation of mast cell proliferation ...positive regulation of myeloid leukocyte differentiation / stem cell factor receptor binding / mast cell migration / positive regulation of hematopoietic stem cell proliferation / positive regulation of hematopoietic progenitor cell differentiation / negative regulation of mast cell apoptotic process / melanocyte migration / positive regulation of melanocyte differentiation / myeloid leukocyte differentiation / positive regulation of mast cell proliferation / mast cell apoptotic process / mast cell proliferation / positive regulation of Ras protein signal transduction / positive regulation of leukocyte migration / neural crest cell migration / embryonic hemopoiesis / Regulation of KIT signaling / ectopic germ cell programmed cell death / hematopoietic progenitor cell differentiation / T cell proliferation / ovarian follicle development / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / Transcriptional and post-translational regulation of MITF-M expression and activity / cytokine activity / filopodium / growth factor activity / Signaling by SCF-KIT / male gonad development / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / lamellipodium / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Ras protein signal transduction / cytoskeleton / cell adhesion / positive regulation of cell population proliferation / extracellular space / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Stem cell factor / Stem cell factor / Growth Hormone; Chain: A; - #10 / Four-helical cytokine-like, core / Growth Hormone; Chain: A; / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJiang, X. / Gurel, O. / Langley, K.E. / Hendrickson, W.A.
CitationJournal: EMBO J. / Year: 2000
Title: Structure of the active core of human stem cell factor and analysis of binding to its receptor kit.
Authors: Jiang, X. / Gurel, O. / Mendiaz, E.A. / Stearns, G.W. / Clogston, C.L. / Lu, H.S. / Osslund, T.D. / Syed, R.S. / Langley, K.E. / Hendrickson, W.A.
History
DepositionJun 4, 1998Processing site: BNL
Revision 1.0Jul 7, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_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_asym_id / _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.pdbx_leaving_atom_flag / _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
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: STEM CELL FACTOR
B: STEM CELL FACTOR
C: STEM CELL FACTOR
D: STEM CELL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6558
Polymers124,2974
Non-polymers3594
Water4,756264
1
A: STEM CELL FACTOR
B: STEM CELL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3873
Polymers62,1482
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-22 kcal/mol
Surface area12440 Å2
MethodPISA
2
C: STEM CELL FACTOR
D: STEM CELL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2695
Polymers62,1482
Non-polymers1203
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-11 kcal/mol
Surface area10940 Å2
MethodPISA
3
C: STEM CELL FACTOR
D: STEM CELL FACTOR
hetero molecules

A: STEM CELL FACTOR
B: STEM CELL FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,6558
Polymers124,2974
Non-polymers3594
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y+1/2,-z+1/21
Buried area5340 Å2
ΔGint-40 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.820, 82.550, 88.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.9153, 0.3684, 0.1628), (0.3571, -0.9292, 0.095), (0.1863, -0.0288, -0.9821)-10.3438, 35.5567, 43.1757
2given(-0.935658, -0.315827, -0.157471), (-0.265278, 0.923709, -0.276386), (0.232747, -0.216829, -0.948058)63.79985, 17.94411, 63.68074
3given(-0.9947, 0.0883, -0.0517), (-0.094, -0.9884, 0.1191), (-0.0406, 0.1234, 0.9915)54.5472, 48.8815, -20.5439
4given(-0.9911, 0.1005, -0.0878), (-0.1178, -0.968, 0.2217), (-0.0627, 0.2301, 0.9711)55.1684, 45.0721, -21.924
5given(-0.9519, -0.2483, 0.1797), (-0.2771, 0.9476, -0.1588), (-0.1309, -0.2009, -0.9708)52.2627, 13.3378, 74.4151
6given(0.9842, 0.1471, -0.0981), (0.1426, -0.9884, -0.0521), (-0.1046, 0.0373, -0.9938)0.5534, 52.6073, 86.741
7given(-0.9554, -0.2442, 0.1661), (-0.2695, 0.9509, -0.1522), (-0.1208, -0.1901, -0.9743)52.8429, 12.5299, 73.7611

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Components

#1: Protein
STEM CELL FACTOR / SCF / SL / MGF / MAST CELL GROWTH FACTOR


Mass: 31074.225 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P21583
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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

Crystal growpH: 7.4 / Details: pH 7.40
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
138 mg/mlprotein1drop
210 mMsodium phosphate1drop
380 mM1dropNaCl
425 %(w/v)PEG4001reservoir
5220 mM1reservoirCaCl2
6100 mMHEPES1reservoir
75-10 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.986
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jul 1, 1995 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.986 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 65689 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Redundancy: 2.75 % / Biso Wilson estimate: 38.5 Å2 / Rsym value: 0.056 / Net I/σ(I): 15.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.23 % / Mean I/σ(I) obs: 1.6 / Rsym value: 0.581 / % possible all: 72
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 72 % / Rmerge(I) obs: 0.581

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MADLSQmodel building
X-PLOR3.1model building
X-PLOR3.1refinement
MADLSQphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
Details: REFINEMENT WAS PERFORMED WITH ANOMALOUS ON; PARAM19_MOD.PRO AND TOPH19_MOD.PRO ARE MODIFIED PARAMETER AND TOPOLOGY FILES OF PARAM19.PRO AND TOPH19.PRO, RESPECTIVELY, FOR SELENOMETHIONYL ...Details: REFINEMENT WAS PERFORMED WITH ANOMALOUS ON; PARAM19_MOD.PRO AND TOPH19_MOD.PRO ARE MODIFIED PARAMETER AND TOPOLOGY FILES OF PARAM19.PRO AND TOPH19.PRO, RESPECTIVELY, FOR SELENOMETHIONYL PROTEINS. NCS RESTRAINTS WERE APPLIED ONLY DURING THE INITIAL REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3016 6 %RANDOM
Rwork0.199 ---
obs0.199 49851 96.6 %-
Displacement parametersBiso mean: 32.1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3517 0 19 264 3800
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.05
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.21.5
X-RAY DIFFRACTIONx_mcangle_it1.62
X-RAY DIFFRACTIONx_scbond_it2.12
X-RAY DIFFRACTIONx_scangle_it2.42.5
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 302 6.4 %
Rwork0.3159 4349 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19_MOD.PROTOPH19_MOD.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3HETEROPARAM19.PARHETERO.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.05

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