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- PDB-3w94: Structure of Oryzias latipes enteropeptidase light chain -

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Basic information

Entry
Database: PDB / ID: 3w94
TitleStructure of Oryzias latipes enteropeptidase light chain
ComponentsEnteropeptidase-1
KeywordsHYDROLASE / SERINE PROTEASE
Function / homology
Function and homology information


serine-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SEA domain profile. / SEA domain / SEA domain ...Scavenger receptor cysteine-rich domain / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / SRCR-like domain / SRCR-like domain superfamily / Scavenger receptor Cys-rich / SEA domain profile. / SEA domain / SEA domain / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Thaumatin, conserved site / Thaumatin family signature. / 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 / 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 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Trypsin-like serine proteases / Concanavalin A-like lectin/glucanase domain superfamily / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesOryzias latipes (Japanese medaka)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å
AuthorsHu, S. / Xu, J. / Wang, H. / Guo, Y.J.
CitationJournal: Protein Cell / Year: 2014
Title: Structure basis for the unique specificity of medaka enteropeptidase light chain.
Authors: Xu, J. / Hu, S. / Wang, X. / Zhao, Z. / Zhang, X. / Wang, H. / Zhang, D. / Guo, Y.
History
DepositionMar 26, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Enteropeptidase-1
B: Enteropeptidase-1


Theoretical massNumber of molelcules
Total (without water)52,0752
Polymers52,0752
Non-polymers00
Water5,278293
1
A: Enteropeptidase-1


Theoretical massNumber of molelcules
Total (without water)26,0371
Polymers26,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Enteropeptidase-1


Theoretical massNumber of molelcules
Total (without water)26,0371
Polymers26,0371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.470, 71.641, 134.433
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Enteropeptidase-1


Mass: 26037.463 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 795-1029
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryzias latipes (Japanese medaka) / Gene: EP-1 / Production host: Escherichia coli (E. coli) / References: UniProt: A4UWM5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.6
Details: 20% PEG 3350, 0.1M sodium acetate trihydrate, 0.1M cadmium chloride hydrate, pH 4.6, VAPOR DIFFUSION, temperature 291.0K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 32262 / % possible obs: 99.7 % / Observed criterion σ(F): 2.9 / Observed criterion σ(I): 8.7
Reflection shellHighest resolution: 2 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.002→40.145 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2409 1631 5.06 %RANDOM
Rwork0.1929 ---
obs0.1954 32203 99.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.002→40.145 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3638 0 0 293 3931
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083740
X-RAY DIFFRACTIONf_angle_d1.2215072
X-RAY DIFFRACTIONf_dihedral_angle_d16.5231332
X-RAY DIFFRACTIONf_chiral_restr0.091532
X-RAY DIFFRACTIONf_plane_restr0.005666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.002-2.06090.26841400.1852246299
2.0609-2.12740.26941230.1832536100
2.1274-2.20350.27281450.1782526100
2.2035-2.29170.24821380.18852494100
2.2917-2.3960.2211270.18732541100
2.396-2.52230.28361130.20652534100
2.5223-2.68030.26841220.21512571100
2.6803-2.88710.30021500.22252532100
2.8871-3.17760.22711350.20642559100
3.1776-3.63710.23641430.19492564100
3.6371-4.58140.2371480.1669256098
4.5814-40.15310.19031470.1953269398
Refinement TLS params.Method: refined / Origin x: 10.0519 Å / Origin y: -16.7015 Å / Origin z: -26.0589 Å
111213212223313233
T0.1202 Å20.0155 Å20.0049 Å2-0.1123 Å2-0.0024 Å2--0.1325 Å2
L0.2262 °20.0192 °20.109 °2-0.1764 °20.0289 °2--0.4668 °2
S0.0145 Å °0.0207 Å °-0.0033 Å °-0.0189 Å °-0.0265 Å °-0.0032 Å °-0.0264 Å °0.0092 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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