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- PDB-2oq5: Crystal structure of DESC1, a new member of the type II transmemb... -

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Basic information

Entry
Database: PDB / ID: 2oq5
TitleCrystal structure of DESC1, a new member of the type II transmembrane serine proteinases family
ComponentsTransmembrane protease, serine 11E
KeywordsHYDROLASE / Type II trans-membrane serine proteinases / trypsin-like serine protease / tumor marker
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / serine-type peptidase activity / cognition / serine-type endopeptidase activity / proteolysis / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, HAT/DESC1 / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / 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 family, serine active site. ...Peptidase S1A, HAT/DESC1 / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / 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 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 / Transmembrane protease serine 11E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.61 Å
AuthorsKyrieleis, O.J.P. / Huber, R. / Madison, E.L. / Jacob, U.
CitationJournal: Febs J. / Year: 2007
Title: Crystal structure of the catalytic domain of DESC1, a new member of the type II transmembrane serine proteinase family.
Authors: Kyrieleis, O.J.P. / Huber, R. / Ong, E. / Oehler, R. / Hunter, M. / Madison, E.L. / Jacob, U.
History
DepositionJan 31, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transmembrane protease, serine 11E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6442
Polymers25,5241
Non-polymers1201
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.900, 70.200, 80.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein Transmembrane protease, serine 11E / Serine protease DESC1 / Transmembrane protease / serine 11E catalytic chain


Mass: 25523.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TMPRSS11E, DESC1 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): SMD 1168
References: UniProt: Q9UL52, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M Tris , 8 % (m/w) PEG 8000 , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→28 Å / Num. all: 36411 / Num. obs: 31409 / % possible obs: 86.3 % / Observed criterion σ(F): 1.6 / Observed criterion σ(I): 1.6 / Redundancy: 4.6 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.79
Reflection shellHighest resolution: 1.6 Å / Num. unique all: 36411

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Enteropeptidase

Resolution: 1.61→28 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1104423.05 / Data cutoff high rms absF: 1104423.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1556 5 %RANDOM
Rwork0.21 ---
all0.21 36411 --
obs0.21 31409 87.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.3368 Å2 / ksol: 0.385118 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--0.2 Å20 Å2
3---0.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.61→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1795 0 9 126 1930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it3.132
X-RAY DIFFRACTIONc_scangle_it4.632.5
LS refinement shellResolution: 1.61→1.7 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.472 185 5.2 %
Rwork0.503 3407 -
obs--60.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5ben.parben.top

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