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- PDB-8iui: Crystal structure of silkworm fibroinase complexed with E-64 -

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Basic information

Entry
Database: PDB / ID: 8iui
TitleCrystal structure of silkworm fibroinase complexed with E-64
ComponentsFibroinase
KeywordsHYDROLASE / Cathepsin / Inhibitor / Complex / Silkworm
Function / homology
Function and homology information


cysteine-type endopeptidase activator activity involved in apoptotic process / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / lysosome / immune response / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Chem-E64 / Fibroinase
Similarity search - Component
Biological speciesBombyx mori (domestic silkworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsGuo, P.C. / Wang, Z. / Zhao, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31970468 China
National Natural Science Foundation of China (NSFC)32030103 China
CitationJournal: To Be Published
Title: Crystal structure of silkworm fibroinase complexed with E64 silworm
Authors: Guo, P.C. / Wang, Z. / Zhao, P.
History
DepositionMar 24, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fibroinase
B: Fibroinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6214
Polymers47,9002
Non-polymers7212
Water3,801211
1
A: Fibroinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3112
Polymers23,9501
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fibroinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3112
Polymers23,9501
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.180, 64.690, 92.910
Angle α, β, γ (deg.)90.000, 97.641, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fibroinase


Mass: 23950.209 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bombyx mori (domestic silkworm) / Production host: Komagataella pastoris (fungus) / References: UniProt: Q6T9Z7
#2: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H30N5O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30% w/v Polyethylene glycol monomethyl ether 2,000, 0.1 M Potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.56→92.09 Å / Num. obs: 58638 / % possible obs: 99.6 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.055 / Rrim(I) all: 0.143 / Net I/σ(I): 8.1
Reflection shellResolution: 1.56→1.6 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.392 / Num. unique obs: 4333 / Rpim(I) all: 0.164 / Rrim(I) all: 0.425 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.56→92.085 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.229 / SU B: 2.928 / SU ML: 0.1 / Average fsc free: 0.8256 / Average fsc work: 0.8373 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.109
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2693 2863 4.884 %
Rwork0.2313 55761 -
all0.233 --
obs-58624 99.58 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 15.376 Å2
Baniso -1Baniso -2Baniso -3
1--1.645 Å2-0 Å20.077 Å2
2---0.904 Å20 Å2
3---2.441 Å2
Refinement stepCycle: LAST / Resolution: 1.56→92.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3360 0 50 211 3621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133486
X-RAY DIFFRACTIONr_bond_other_d0.0010.0183062
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.6364722
X-RAY DIFFRACTIONr_angle_other_deg1.4411.5887084
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2275434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00224.167192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24515546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9721512
X-RAY DIFFRACTIONr_chiral_restr0.0820.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024118
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02802
X-RAY DIFFRACTIONr_nbd_refined0.2160.2700
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23117
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21733
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2179
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1420.216
X-RAY DIFFRACTIONr_nbd_other0.170.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.224
X-RAY DIFFRACTIONr_mcbond_it1.2121.481742
X-RAY DIFFRACTIONr_mcbond_other1.2041.4791741
X-RAY DIFFRACTIONr_mcangle_it1.8682.2182174
X-RAY DIFFRACTIONr_mcangle_other1.8692.2182175
X-RAY DIFFRACTIONr_scbond_it1.9351.7331744
X-RAY DIFFRACTIONr_scbond_other1.9351.7311743
X-RAY DIFFRACTIONr_scangle_it2.9532.5122548
X-RAY DIFFRACTIONr_scangle_other2.9522.5142549
X-RAY DIFFRACTIONr_lrange_it3.74117.7293971
X-RAY DIFFRACTIONr_lrange_other3.72217.6673952
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.56-1.6010.3422120.33341210.33443840.5840.58398.83670.328
1.601-1.6440.3411740.32639660.32741800.5740.699.04310.32
1.644-1.6920.3491970.31338710.31441070.6860.70899.05040.305
1.692-1.7440.3062110.27837800.2840240.8010.81599.17990.27
1.744-1.8010.2762070.25435990.25538350.8550.86499.24380.244
1.801-1.8640.2742030.23435350.23637440.870.88599.83970.223
1.864-1.9350.2741720.23834350.23936160.8740.88599.75110.226
1.935-2.0140.2861530.23533130.23834710.8710.88299.85590.225
2.014-2.1030.3031600.2431900.24333580.8590.87699.76180.229
2.103-2.2060.2711650.22430290.22731950.8820.999.96870.216
2.206-2.3250.2741490.2128910.21330410.8930.91499.96710.204
2.325-2.4660.2891280.21327360.21628650.8830.91399.96510.207
2.466-2.6360.241990.21726070.21727080.9080.91399.92610.211
2.636-2.8470.241470.22123600.22225110.9080.90799.84070.22
2.847-3.1190.2551240.21421990.21623240.9080.92599.9570.218
3.119-3.4860.2121050.2120160.2121210.9270.9331000.216
3.486-4.0250.205850.19517700.19518590.9340.94499.78480.206
4.025-4.9270.257910.19415000.19715920.9140.94799.93720.212
4.927-6.9580.332560.24111680.24412340.8910.92499.18960.263
6.958-92.0850.256250.2446750.2447020.9460.92199.71510.272

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