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- PDB-3ncl: Crystal Structure of MT-SP1 bound to Benzamidine Phosphonate Inhibitor -

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Basic information

Entry
Database: PDB / ID: 3ncl
TitleCrystal Structure of MT-SP1 bound to Benzamidine Phosphonate Inhibitor
ComponentsSuppressor of tumorigenicity 14 protein
KeywordsHYDROLASE / proteinase-inhibitor complex / serine proteinase / benzamidine / phosphonate / serine endopeptidases
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / 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 ...matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / 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 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
phenyl (4-carbamimidoylbenzyl)phosphonate / FORMIC ACID / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.19 Å
AuthorsRay, M. / Brown, C. / Egea, P.
CitationJournal: Chem.Biol. / Year: 2011
Title: Peptide length and leaving-group sterics influence potency of Peptide phosphonate protease inhibitors.
Authors: Brown, C.M. / Ray, M. / Eroy-Reveles, A.A. / Egea, P. / Tajon, C. / Craik, C.S.
History
DepositionJun 4, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
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_conn / 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_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: Suppressor of tumorigenicity 14 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8765
Polymers26,4481
Non-polymers4284
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.915, 80.240, 40.539
Angle α, β, γ (deg.)90.00, 95.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-282-

HOH

21A-304-

HOH

31A-386-

HOH

41A-397-

HOH

51A-471-

HOH

61A-621-

HOH

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Components

#1: Protein Suppressor of tumorigenicity 14 protein / Serine protease 14 / Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine ...Serine protease 14 / Matriptase / Membrane-type serine protease 1 / MT-SP1 / Prostamin / Serine protease TADG-15 / Tumor-associated differentially-expressed gene 15 protein


Mass: 26447.689 Da / Num. of mol.: 1 / Fragment: peptidase S1 domain / Mutation: C731S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5Y6, matriptase
#2: Chemical ChemComp-CCZ / phenyl (4-carbamimidoylbenzyl)phosphonate / phenyl Benzamidine Phosphonate


Mass: 290.254 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H15N2O3P
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / 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: 2.29 Å3/Da / Density % sol: 46.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.0 M Na Formate, 25mM FeCl3, 20% glycerol cryoprotectant, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.19→54.6 Å / Num. all: 58355 / Num. obs: 58355 / % possible obs: 76.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 21
Reflection shellResolution: 1.19→1.25 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.015 / Mean I/σ(I) obs: 5 / Rsym value: 0.15

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHENIX1.6.3_473refinement
PDB_EXTRACT3.1data extraction
ELVESrefinement
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BN9

3bn9


Resolution: 1.19→40.12 Å / Occupancy max: 1 / Occupancy min: 0.17 / SU ML: 0.13 / σ(F): 1.51 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1563 1530 2.63 %
Rwork0.1332 --
obs0.1339 58173 76.26 %
all-58355 -
Solvent computationShrinkage radii: 0 Å / VDW probe radii: 0.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.349 Å2 / ksol: 0.556 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0079 Å2-0 Å21.1686 Å2
2---0.4515 Å20 Å2
3----0.5564 Å2
Refinement stepCycle: LAST / Resolution: 1.19→40.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1856 0 29 398 2283
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011973
X-RAY DIFFRACTIONf_angle_d1.3982684
X-RAY DIFFRACTIONf_dihedral_angle_d14.26705
X-RAY DIFFRACTIONf_chiral_restr0.081280
X-RAY DIFFRACTIONf_plane_restr0.007355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1894-1.23190.3541230.2539729X-RAY DIFFRACTION10
1.2319-1.28120.238690.16582131X-RAY DIFFRACTION29
1.2812-1.33960.1941950.14263720X-RAY DIFFRACTION50
1.3396-1.41020.15891440.13495548X-RAY DIFFRACTION75
1.4102-1.49850.1721970.12217360X-RAY DIFFRACTION99
1.4985-1.61420.16871990.1177395X-RAY DIFFRACTION100
1.6142-1.77670.15372000.12397422X-RAY DIFFRACTION100
1.7767-2.03380.14842010.12157427X-RAY DIFFRACTION100
2.0338-2.56230.15541990.12397423X-RAY DIFFRACTION100
2.5623-40.14280.15132030.14787488X-RAY DIFFRACTION99

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