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- PDB-3hmr: Crystal structure of the N-terminal fragment (31-127) of the mous... -

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Basic information

Entry
Database: PDB / ID: 3hmr
TitleCrystal structure of the N-terminal fragment (31-127) of the mouse hepatocyte growth factor/scatter factor
ComponentsHepatocyte growth factor
KeywordsHORMONE / HGF/SF / hormone/growth factor / Disulfide bond / Glycoprotein / Growth factor / Kringle / Pyrrolidone carboxylic acid / Serine protease homolog
Function / homology
Function and homology information


positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 ...positive regulation of neuron projection regeneration / MET Receptor Activation / Drug-mediated inhibition of MET activation / MET interacts with TNS proteins / MET activates STAT3 / MET activates PI3K/AKT signaling / MET activates RAS signaling / MET activates PTPN11 / MET activates PTK2 signaling / MET activates RAP1 and RAC1 / MET receptor recycling / Negative regulation of MET activity / RAF/MAP kinase cascade / regulation of p38MAPK cascade / positive regulation of myelination / PIP3 activates AKT signaling / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / Platelet degranulation / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / hepatocyte growth factor receptor signaling pathway / myoblast proliferation / positive regulation of DNA biosynthetic process / cellular response to hepatocyte growth factor stimulus / negative regulation of release of cytochrome c from mitochondria / chemoattractant activity / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of peptidyl-serine phosphorylation / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / cell chemotaxis / liver development / epithelial cell proliferation / growth factor activity / cell morphogenesis / negative regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cell migration / positive regulation of protein phosphorylation / signaling receptor binding / protein-containing complex binding / negative regulation of apoptotic process / proteolysis / extracellular space / extracellular region / identical protein binding
Similarity search - Function
Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle ...Hepatocyte growth factor / Hepatocyte growth factor/Macrophage stimulatory protein / Hepatocyte Growth Factor / Hepatocyte Growth Factor / 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 / 3-Layer(bba) Sandwich / 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 / Alpha Beta
Similarity search - Domain/homology
Hepatocyte growth factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTolbert, W.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Structural basis for agonism and antagonism of hepatocyte growth factor.
Authors: Tolbert, W.D. / Daugherty-Holtrop, J. / Gherardi, E. / Vande Woude, G. / Xu, H.E.
History
DepositionMay 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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: Hepatocyte growth factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,7792
Polymers11,6821
Non-polymers961
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.420, 62.420, 58.890
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Hepatocyte growth factor / / Scatter factor / SF / Hepatopoeitin-A / Hepatocyte growth factor alpha chain / Hepatocyte growth ...Scatter factor / SF / Hepatopoeitin-A / Hepatocyte growth factor alpha chain / Hepatocyte growth factor beta chain


Mass: 11682.447 Da / Num. of mol.: 1 / Fragment: N-terminal domain: UNP residues 31-127
Source method: isolated from a genetically manipulated source
Details: Expressed as a thioredoxin fusion protein / Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hgf / Plasmid: pET-Duet1/Trx / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE) / References: UniProt: Q08048
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O

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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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50 mM Ammonium sulfate, 24-30% PEG 2000, 50 mM HEPES pH 8.0, 5% 2-Methyl-2,4-pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 22, 2006
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 8117 / Num. obs: 8117 / % possible obs: 90.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 7.7 Å2 / Rmerge(I) obs: 0.133 / Rsym value: 0.133 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 1.7 / Num. unique all: 877 / Rsym value: 0.415 / % possible all: 53.9

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Processing

Software
NameClassification
SERGUIdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NK1

1nk1


Resolution: 2→39.82 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 80574.06 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.265 829 10.8 %RANDOM
Rwork0.211 ---
all0.228 8117 --
obs0.211 7699 86.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1047 Å2 / ksol: 0.395291 e/Å3
Displacement parametersBiso mean: 30.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å21.98 Å20 Å2
2--0.73 Å20 Å2
3----1.46 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→39.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms748 0 5 82 835
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.971.5
X-RAY DIFFRACTIONc_mcangle_it3.352
X-RAY DIFFRACTIONc_scbond_it2.472
X-RAY DIFFRACTIONc_scangle_it3.822.5
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.285 47 11.8 %
Rwork0.272 738 -
obs-429 53.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_rep.top
X-RAY DIFFRACTION3ion.paramion.top

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