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- PDB-3p8g: Crystal Structure of MT-SP1 in complex with benzamidine -

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Basic information

Entry
Database: PDB / ID: 3p8g
TitleCrystal Structure of MT-SP1 in complex with benzamidine
ComponentsST14 protein
KeywordsHYDROLASE
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity ...matriptase / epithelial cell morphogenesis involved in placental branching / Formation of the cornified envelope / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / basolateral plasma membrane / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / plasma membrane
Similarity search - Function
Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily ...Peptidase S1A, matripase / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / 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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / GLUTATHIONE / ST14 protein / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsYuan, C. / Huang, M. / Chen, L.
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: Structure of catalytic domain of Matriptase in complex with Sunflower trypsin inhibitor-1.
Authors: Yuan, C. / Chen, L. / Meehan, E.J. / Daly, N. / Craik, D.J. / Huang, M. / Ngo, J.C.
History
DepositionOct 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Nov 1, 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_conn / 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_conn.pdbx_leaving_atom_flag / _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: ST14 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,44210
Polymers26,4781
Non-polymers9649
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.888, 141.701, 51.995
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1076-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ST14 protein / Membrane-type serine protease 1


Mass: 26477.783 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP 182-422) / Mutation: N164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pPICZalpha / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): X33
References: UniProt: Q8WVC1, UniProt: Q9Y5Y6*PLUS, matriptase

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Non-polymers , 5 types, 321 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Chemical ChemComp-GSH / GLUTATHIONE


Mass: 307.323 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N3O6S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.33 Å3/Da / Density % sol: 47.13 % / Mosaicity: 0.372 °
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris.HCl, pH 8.0, 1.5M ammonium sulfate, 3% ethanol, vapor diffusion, hanging drop, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.04 Å
DetectorDetector: CCD / Date: Jan 30, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.2→70.89 Å / Num. obs: 70901 / % possible obs: 91.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.106 / Χ2: 0.959 / Net I/σ(I): 5.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.2-1.242.90.48572360.33194.6
1.24-1.294.20.44276040.34199.3
1.29-1.354.80.36774920.363197.8
1.35-1.426.20.30876750.4161100
1.42-1.515.90.24876460.466199.5
1.51-1.636.90.18177190.5761100
1.63-1.796.90.13476960.7471100
1.79-2.056.30.10751681.283166.7
2.05-2.596.80.0960501.906177.4
2.59-506.30.07266152.831181.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EAX

1eax


Resolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.1 / SU B: 1.039 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 3553 5 %RANDOM
Rwork0.1428 ---
obs0.1446 70879 91.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 53.3 Å2 / Biso mean: 16.0191 Å2 / Biso min: 8.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.36 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1865 0 60 312 2237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0212034
X-RAY DIFFRACTIONr_angle_refined_deg2.141.9642771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5315254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23923.59689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99215304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4061513
X-RAY DIFFRACTIONr_chiral_restr0.1470.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211596
X-RAY DIFFRACTIONr_mcbond_it2.2511.51240
X-RAY DIFFRACTIONr_mcangle_it3.12821998
X-RAY DIFFRACTIONr_scbond_it4.5473794
X-RAY DIFFRACTIONr_scangle_it6.1154.5773
X-RAY DIFFRACTIONr_rigid_bond_restr2.55632034
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 241 -
Rwork0.227 4995 -
all-5236 -
obs--92.64 %

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