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- PDB-1p57: Extracellular domain of human hepsin -

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Basic information

Entry
Database: PDB / ID: 1p57
TitleExtracellular domain of human hepsin
Components(Serine protease hepsin) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / srcr / scavenger receptor cysteine-rich domain / serine protease / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation ...hepsin / pilomotor reflex / Signaling by MST1 / positive regulation of thyroid hormone generation / cochlea morphogenesis / serine-type exopeptidase activity / positive regulation of plasminogen activation / basement membrane disassembly / detection of mechanical stimulus involved in sensory perception of sound / MET Receptor Activation / response to thyroid hormone / negative regulation of epithelial to mesenchymal transition / positive regulation by host of viral transcription / positive regulation of hepatocyte proliferation / potassium ion transmembrane transport / serine-type peptidase activity / negative regulation of epithelial cell proliferation / cell-cell junction / peptidase activity / regulation of cell shape / positive regulation of cell growth / apical plasma membrane / serine-type endopeptidase activity / neuronal cell body / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / cell surface / proteolysis / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Hepsin, SRCR domain / Hepsin, SRCR domain / Mac-2 Binding Protein / SRCR-like domain / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family ...Hepsin, SRCR domain / Hepsin, SRCR domain / Mac-2 Binding Protein / SRCR-like domain / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / 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 / Roll / Peptidase S1, PA clan / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-CR4 / Serine protease hepsin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsSomoza, J.R. / Ho, J.D. / Luong, C. / Sprengeler, P.A. / Mortara, K. / Shrader, W.D. / Sperandio, D. / Chan, H. / McGrath, M.E. / Katz, B.A.
CitationJournal: Structure / Year: 2003
Title: The Structure of the Extracellular Region of Human Hepsin Reveals a Serine Protease Domain and a Novel Scavenger Receptor Cysteine-Rich (SRCR) Domain
Authors: Somoza, J.R. / Ho, J.D. / Luong, C. / Ghate, M. / Sprengeler, P.A. / Mortara, K. / Shrader, W.D. / Sperandio, D. / Chan, H. / McGrath, M.E. / Katz, B.A.
History
DepositionApr 25, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2016Group: Derived calculations / Structure summary
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine protease hepsin
B: Serine protease hepsin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3483
Polymers40,0952
Non-polymers2521
Water4,990277
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.800, 47.800, 63.100
Angle α, β, γ (deg.)90.00, 104.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Serine protease hepsin / Transmembrane protease / serine 1


Mass: 12522.299 Da / Num. of mol.: 1 / Fragment: Residues 1-114 (Light chain) / Mutation: N112A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / Strain (production host): KM71
References: UniProt: P05981, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Protein Serine protease hepsin / Transmembrane protease / serine 1


Mass: 27573.111 Da / Num. of mol.: 1 / Fragment: Residues 16-255 (Heavy chain)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Pichia pastoris (fungus) / Strain (production host): KM71
References: UniProt: P05981, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#3: Chemical ChemComp-CR4 / 2-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}BENZENOLATE / CRA_1144


Mass: 252.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N4O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 291 K / pH: 7.5
Details: ammonium fluoride, PEG 3350, sodium cacodylate, tris, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.5, pH 7.50
Crystal grow
*PLUS
Temperature: 17 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 Mammonium fluoride1reservoir
220-25 %PEG33501reservoir
30.1 Msodium cacodylate1reservoirpH6.2
410 mg/mlprotein1drop
50.6 mMinhibitor1drop
650 mMTris-HCl1droppH7.6

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 9, 2002 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→25.7 Å / Num. obs: 30969 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 3.82 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.4
Reflection shellResolution: 1.75→1.83 Å / Redundancy: 2.11 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 1.7 / % possible all: 53.7
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 25.7 Å / Num. obs: 31195 / % possible obs: 96.1 % / Num. measured all: 93729 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 53.3 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EKB

1ekb


Resolution: 1.75→25.7 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0.7 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.206 3107 -RANDOM
Rwork0.186 ---
obs0.186 30969 90 %-
all-31246 --
Refinement stepCycle: LAST / Resolution: 1.75→25.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 19 277 3009
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.18
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg3.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.75→1.83 Å /
RfactorNum. reflection
Rfree0.401 199
Rwork0.371 -
Refinement
*PLUS
Lowest resolution: 7 Å / Num. reflection Rfree: 3114 / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.018

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