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- PDB-1yc0: short form HGFA with first Kunitz domain from HAI-1 -

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Basic information

Entry
Database: PDB / ID: 1yc0
Titleshort form HGFA with first Kunitz domain from HAI-1
Components
  • Hepatocyte growth factor activator
  • Kunitz-type protease inhibitor 1
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases ...epithelium development / Signaling by MST1 / positive regulation of glial cell differentiation / negative regulation of neural precursor cell proliferation / branching involved in labyrinthine layer morphogenesis / placenta blood vessel development / MET Receptor Activation / cellular response to BMP stimulus / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / epidermis development / rough endoplasmic reticulum / serine-type peptidase activity / extracellular matrix organization / neural tube closure / serine-type endopeptidase inhibitor activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / Coagulation factor XII/hepatocyte growth factor activator / MANSC domain profile. / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain ...MANEC domain / Seven cysteines, N-terminal / MANEC / MANSC domain / Coagulation factor XII/hepatocyte growth factor activator / MANSC domain profile. / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Pancreatic trypsin inhibitor Kunitz domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Factor Xa Inhibitor / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Epidermal growth factor-like domain. / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Immunoglobulin-like fold / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / Kunitz-type protease inhibitor 1 / Hepatocyte growth factor activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsShia, S. / Stamos, J. / Kirchhofer, D. / Fan, B. / Wu, J. / Corpuz, R.T. / Santell, L. / Lazarus, R.A. / Eigenbrot, C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Conformational lability in serine protease active sites: structures of hepatocyte growth factor activator (HGFA) alone and with the inhibitory domain from HGFA inhibitor-1B.
Authors: Shia, S. / Stamos, J. / Kirchhofer, D. / Fan, B. / Wu, J. / Corpuz, R.T. / Santell, L. / Lazarus, R.A. / Eigenbrot, C.
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 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 activator
I: Kunitz-type protease inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9213
Polymers39,8262
Non-polymers951
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-13 kcal/mol
Surface area14310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.218, 76.218, 176.236
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hepatocyte growth factor activator / HGF activator / HGFA


Mass: 30885.154 Da / Num. of mol.: 1 / Fragment: sequence database residues 373-655
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HGFAC / Plasmid: pAcGP67A / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Kunitz-type protease inhibitor 1 / Hepatocyte growth factor activator inhibitor type 1 / HAI-1 / KUNITZ DOMAIN FROM HAI-1


Mass: 8941.067 Da / Num. of mol.: 1 / Fragment: sequence database residues 245-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SPINT1, HAI1 / Plasmid: pKD1 / Production host: Escherichia coli (E. coli) / Strain (production host): 58F3 / References: UniProt: O43278
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.71 Å3/Da / Density % sol: 66.85 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 50% MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 14, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 17975 / Num. obs: 17975 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 4.3 % / Biso Wilson estimate: 55 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 17
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1857 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.07refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FAK

1fak


Resolution: 2.6→43.85 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 6.764 / SU ML: 0.143 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: restrained atomic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21811 966 5.1 %RANDOM
Rwork0.19492 ---
all0.2007 18983 --
obs0.19611 18983 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.519 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.2 Å20 Å2
2--0.4 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.6→43.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 5 119 2553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212511
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9393409
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9445310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75422.895114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88815385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2171517
X-RAY DIFFRACTIONr_chiral_restr0.0720.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021954
X-RAY DIFFRACTIONr_nbd_refined0.2280.21171
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2164
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.28
X-RAY DIFFRACTIONr_mcbond_it2.5622.51551
X-RAY DIFFRACTIONr_mcangle_it4.49552485
X-RAY DIFFRACTIONr_scbond_it3.052.5960
X-RAY DIFFRACTIONr_scangle_it4.7665924
LS refinement shellResolution: 2.6→2.74 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.345 142
Rwork0.287 2566
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84210.0928-0.33090.9059-0.31943.99270.14350.0345-0.0550.132-0.14120.12420.1331-0.1698-0.00230.1936-0.0201-0.00610.0178-0.04120.1118-12.654255.108457.4159
20.6342-0.2395-0.00570.81790.15520.59250.07360.0190.0401-0.0661-0.0655-0.03010.0243-0.014-0.00810.16430.0906-0.01710.0506-0.00820.0851-2.735665.445933.0609
37.77875.11222.79934.8109-2.407412.33280.14421.8066-0.6428-0.1984-0.113-1.75610.20571.8333-0.03120.20730.18960.12340.4065-0.00680.239210.263166.823119.1141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1IB238 - 30310 - 75
2X-RAY DIFFRACTION2AA408 - 64636 - 274
3X-RAY DIFFRACTION3AA393 - 40021 - 28

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