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- PDB-3hmt: Crystal structure of the N-terminal fragment (28-126) of the huma... -

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Basic information

Entry
Database: PDB / ID: 3hmt
TitleCrystal structure of the N-terminal fragment (28-126) of the human hepatocyte growth factor/scatter factor, trigonal crystal form
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


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 / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / 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 / skeletal muscle cell proliferation / negative regulation of hydrogen peroxide-mediated programmed cell death / 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 / cellular response to hepatocyte growth factor stimulus / positive regulation of DNA biosynthetic process / 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 / liver development / platelet alpha granule lumen / 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 / PIP3 activates AKT signaling / Platelet degranulation / mitotic cell cycle / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / Hepatocyte Growth Factor / Hepatocyte Growth Factor / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain ...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 speciesHomo sapiens (human)
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 1.2Sep 6, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Nov 27, 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
B: Hepatocyte growth factor


Theoretical massNumber of molelcules
Total (without water)23,5892
Polymers23,5892
Non-polymers00
Water2,612145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hepatocyte growth factor


Theoretical massNumber of molelcules
Total (without water)11,7951
Polymers11,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Hepatocyte growth factor


Theoretical massNumber of molelcules
Total (without water)11,7951
Polymers11,7951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.850, 38.850, 103.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: 11794.679 Da / Num. of mol.: 2 / Fragment: N-terminal domain: UNP residues 28-126
Source method: isolated from a genetically manipulated source
Details: Expressed as a thioredoxin fusion protein / Source: (gene. exp.) Homo sapiens (human) / Gene: HGF, HPTA / Plasmid: pET-Duet1/Trx / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B(DE) / References: UniProt: P14210
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 1.92 Å3/Da / Density % sol: 35.78 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M sodium malonate pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 31, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→50 Å / Num. all: 23656 / Num. obs: 23656 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 9.5 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 14.4
Reflection shellResolution: 1.96→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / Num. unique all: 1274 / Rsym value: 0.24 / % possible all: 87.6

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Processing

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

1nk1


Resolution: 2→34.56 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 416044.98 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1976 9.2 %RANDOM
Rwork0.193 ---
all0.206 23656 --
obs0.193 21584 91.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.2688 Å2 / ksol: 0.416442 e/Å3
Displacement parametersBiso mean: 22 Å2
Baniso -1Baniso -2Baniso -3
1--0.53 Å20.55 Å20 Å2
2---0.53 Å20 Å2
3---1.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2→34.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1496 0 0 145 1641
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.215 40 8.7 %
Rwork0.2 2838 -
obs-412 78.4 %
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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