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- PDB-3p8f: Crystal Structure of MT-SP1 in complex with SFTI-1 -

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Basic information

Entry
Database: PDB / ID: 3p8f
TitleCrystal Structure of MT-SP1 in complex with SFTI-1
Components
  • ST14 protein
  • Trypsin inhibitor 1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / protein-inhibitor complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process ...matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / negative regulation of endopeptidase activity / endopeptidase inhibitor activity / keratinocyte differentiation / serine-type peptidase activity / neural tube closure / protein catabolic process / serine-type endopeptidase inhibitor activity / basolateral plasma membrane / protease binding / 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
Trypsin inhibitor 1 / GLUTATHIONE / Trypsin inhibitor 1 / ST14 protein / Suppressor of tumorigenicity 14 protein
Similarity search - Component
Biological speciesHomo sapiens (human)
Helianthus annuus (common sunflower)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 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 10, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Non-polymer description
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ST14 protein
I: Trypsin inhibitor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3213
Polymers28,0142
Non-polymers3071
Water1,820101
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-13 kcal/mol
Surface area10660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.862, 75.862, 94.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 26477.783 Da / Num. of mol.: 1 / Fragment: catalytic domain (UNP RESIDUES 182-422) / Mutation: N164Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ST14 / Plasmid: pPICZalpha / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): X33
References: UniProt: Q8WVC1, UniProt: Q9Y5Y6*PLUS, matriptase
#2: Protein/peptide Trypsin inhibitor 1 / / SFTI-1 /


Type: PolypeptidePeptide / Class: Trypsin inhibitor / Mass: 1535.829 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 40-53 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Helianthus annuus (common sunflower) / References: UniProt: Q4GWU5, Trypsin inhibitor 1
#3: Chemical ChemComp-GSH / GLUTATHIONE / Glutathione


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


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.42 Å3/Da / Density % sol: 49.1 % / Mosaicity: 0.34 °
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris.HCl pH 8.0, 22% PEG 8K, 20mM CaCl2, 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: Jul 10, 2008
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2→59.03 Å / Num. obs: 19001 / % possible obs: 98.9 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.076 / Χ2: 1.065 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.0711.10.52618620.3931100
2.07-2.1513.30.3718810.4121100
2.15-2.2513.40.28218810.5281100
2.25-2.3713.50.20418930.617199.9
2.37-2.5213.80.16218920.7951100
2.52-2.7113.40.1218850.966199.9
2.71-2.99130.09519121.242199.8
2.99-3.4211.70.07719131.929199.2
3.42-4.319.60.05919162.403197.3
4.31-508.20.04519662.2193.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
PHENIX1.7.1_743refinement
RefinementResolution: 2→25.794 Å / SU B: 10.538 / SU ML: 0.68 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 22.15 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 964 5.09 %RANDOM
Rwork0.1918 ---
obs0.1942 17987 98.86 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.039 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.0254 Å2-0 Å20 Å2
2---1.0254 Å2-0 Å2
3---2.0508 Å2
Refinement stepCycle: LAST / Resolution: 2→25.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1969 0 20 101 2090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032047
X-RAY DIFFRACTIONf_angle_d0.6432777
X-RAY DIFFRACTIONf_dihedral_angle_d14.188733
X-RAY DIFFRACTIONf_chiral_restr0.045292
X-RAY DIFFRACTIONf_plane_restr0.003366
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9999-2.10530.35351340.3027253199
2.1053-2.23720.32351540.24462527100
2.2372-2.40980.30741380.22852537100
2.4098-2.65210.26571630.22292545100
2.6521-3.03530.2681380.20822597100
3.0353-3.82220.25041370.1841258299
3.8222-25.7960.17981000.1637266595
Refinement TLS params.Method: refined / Origin x: -9.6529 Å / Origin y: -20.4148 Å / Origin z: -21.1565 Å
111213212223313233
T0.2387 Å20.0355 Å20.0781 Å2-0.3681 Å20.0911 Å2--0.3292 Å2
L2.6626 °20.413 °20.2045 °2-3.9208 °2-1.2449 °2--4.5134 °2
S0.2017 Å °0.0022 Å °0.1711 Å °-0.2827 Å °0.0408 Å °0.1056 Å °0.0718 Å °-0.308 Å °-0.1825 Å °
Refinement TLS groupSelection details: all

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