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- PDB-7ocl: K1K1, a potent recombinant minimal hepatocyte growth factor/scatt... -

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Basic information

Entry
Database: PDB / ID: 7ocl
TitleK1K1, a potent recombinant minimal hepatocyte growth factor/scatter factor mimic
ComponentsHepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain
KeywordsDE NOVO PROTEIN / MET receptor agonist / HGF/SF kringle 1 dimer / HGF/SF-derived recombinant protein / MET-activator / regeneration of epithelial tissue and organs / engineered growth factor
Function / homology
Function and homology information


regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / skeletal muscle cell proliferation / MET Receptor Activation / MET interacts with TNS proteins / hepatocyte growth factor receptor signaling pathway / MET receptor recycling ...regulation of p38MAPK cascade / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Drug-mediated inhibition of MET activation / MET activates STAT3 / negative regulation of hydrogen peroxide-mediated programmed cell death / skeletal muscle cell proliferation / MET Receptor Activation / MET interacts with TNS proteins / hepatocyte growth factor receptor signaling pathway / MET receptor recycling / MET activates PTPN11 / MET activates RAP1 and RAC1 / myoblast proliferation / MET activates PI3K/AKT signaling / MET activates PTK2 signaling / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / chemoattractant activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / epithelial to mesenchymal transition / positive regulation of osteoblast differentiation / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / Interleukin-7 signaling / negative regulation of autophagy / platelet alpha granule lumen / liver development / epithelial cell proliferation / cell chemotaxis / growth factor activity / Negative regulation of MET activity / cell morphogenesis / negative regulation of inflammatory response / Constitutive Signaling by Aberrant PI3K in Cancer / Platelet degranulation / PIP3 activates AKT signaling / mitotic cell cycle / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Interleukin-4 and Interleukin-13 signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / positive regulation of cell migration / signaling receptor binding / negative regulation of apoptotic process / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / membrane
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
Authorsde Jonge, H. / de Nola, G. / Gherardi, E.
CitationJournal: Life Sci Alliance / Year: 2022
Title: Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent MET receptor agonist.
Authors: de Nola, G. / Leclercq, B. / Mougel, A. / Taront, S. / Simonneau, C. / Forneris, F. / Adriaenssens, E. / Drobecq, H. / Iamele, L. / Dubuquoy, L. / Melnyk, O. / Gherardi, E. / de Jonge, H. / Vicogne, J.
History
DepositionApr 27, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 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: Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain
B: Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain


Theoretical massNumber of molelcules
Total (without water)38,4652
Polymers38,4652
Non-polymers00
Water4,630257
1
A: Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain


Theoretical massNumber of molelcules
Total (without water)19,2331
Polymers19,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain


Theoretical massNumber of molelcules
Total (without water)19,2331
Polymers19,2331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.570, 58.750, 65.940
Angle α, β, γ (deg.)90.000, 108.220, 90.000
Int Tables number4
Space group name H-MP1211
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Hepatocyte growth factor alpha chain,Hepatocyte growth factor alpha chain


Mass: 19232.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Production host: Escherichia coli (E. coli) / References: UniProt: P14210
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.19 Å3/Da / Density % sol: 43.74 % / Description: Hexagonal shaped
Crystal growTemperature: 290.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Tris/Bicine pH 8.5, 30 mM Sodium nitrate, 30 mM Sodium phosphate dibasic, 30 mM Ammonium sulfate, 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD
Temp details: Inside fridge-like incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.953725 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953725 Å / Relative weight: 1
ReflectionResolution: 1.61→43.29 Å / Num. obs: 42914 / % possible obs: 99.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 20.25 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.074 / Rrim(I) all: 0.172 / Net I/σ(I): 4.6 / Num. measured all: 224081 / Scaling rejects: 25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.61-1.675.22.1442159941790.4541.0482.3920.699.8
6.24-43.294.90.0838057810.9280.040.0911.999.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2-4158refinement
Aimlessdata scaling
PHASERphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Kringle 1

Resolution: 1.8→43.29 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2271 1442 4.7 %
Rwork0.1966 29271 -
obs0.1981 30713 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.21 Å2 / Biso mean: 32.9721 Å2 / Biso min: 10.88 Å2
Refinement stepCycle: final / Resolution: 1.8→43.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2637 0 0 257 2894
Biso mean---35.05 -
Num. residues----336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.860.29971400.287929173057100
1.86-1.940.30171460.246129093055100
1.94-2.030.30861400.234228973037100
2.03-2.130.25021470.209929213068100
2.13-2.270.24141450.203129283073100
2.27-2.440.2281450.189228943039100
2.44-2.690.20061440.192629393083100
2.69-3.080.22641440.19129403084100
3.08-3.880.18871450.171729403085100
3.88-43.290.21611460.18652986313299

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