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- PDB-6i1m: Secreted type 1 cystatin from Fasciola hepatica -

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Basic information

Entry
Database: PDB / ID: 6i1m
TitleSecreted type 1 cystatin from Fasciola hepatica
ComponentsCystatin
KeywordsHydrolase inhibitor / cystatin / stefin / protease inhibitor / fasciola hepatica
Function / homologyCystatin superfamily / IODIDE ION / Type-1 cystatin cysteine protease inhibitor / Cystatin
Function and homology information
Biological speciesFasciola hepatica (liver fluke)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.6 Å
AuthorsBusa, M. / Rezacova, P. / Pachl, P. / Stefanic, S. / Mares, M.
Funding support Czech Republic, 3items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729 Czech Republic
Czech Academy of Sciences61388963 Czech Republic
Ministry of Education, Youth and Sports of the Czech RepublicLO1304 Czech Republic
CitationJournal: J.Biol.Chem. / Year: 2023
Title: An evolutionary molecular adaptation of an unusual stefin from the liver fluke Fasciola hepatica redefines the cystatin superfamily.
Authors: Busa, M. / Matouskova, Z. / Bartosova-Sojkova, P. / Pachl, P. / Rezacova, P. / Eichenberger, R.M. / Deplazes, P. / Horn, M. / Stefanic, S. / Mares, M.
History
DepositionOct 29, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2023Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 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: Cystatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,0533
Polymers9,7991
Non-polymers2542
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area5800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.878, 67.177, 44.493
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-102-

IOD

21A-273-

HOH

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Components

#1: Protein Cystatin


Mass: 9799.197 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: IRG: N-terminal cloning artifact AAAHHHHHH: C-terminal His-tag E36V, I54T: natural mutations found in the sequence (compared to GenBank AAV68752.1)
Source: (gene. exp.) Fasciola hepatica (liver fluke) / Gene: Cyt / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: Q17TZ2, UniProt: A0A2H1BUS1*PLUS
#2: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.1 Å3/Da / Density % sol: 41.43 % / Description: very small needles in phase separation
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M Ammonium Sulfate 0.1M Sodium Iodide 0.1M Sodium HEPES 7.5 5% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184, 1.5
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Mar 29, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.51
ReflectionResolution: 1.6→46.67 Å / Num. obs: 13043 / % possible obs: 98.4 % / Redundancy: 6.717 % / Biso Wilson estimate: 26.772 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.158 / Rrim(I) all: 0.172 / Χ2: 1.17 / Net I/σ(I): 7.94 / Num. measured all: 87605
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.696.5721.9210.8820580.4342.08697.8
1.69-1.817.0371.2881.4819820.6851.39199.9
1.81-1.966.7810.6952.8218140.9170.75297.8
1.96-2.146.7640.4094.7617060.9430.44499.8
2.14-2.396.9650.2617.2814740.9780.28394.4
2.39-2.766.6860.16410.5413690.990.17899.6
2.76-3.386.7970.0918.4711780.9960.09799.1
3.38-4.776.1490.05925.679090.9970.06598.3
4.77-46.675.9260.05227.575530.9980.05799.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.6→46.67 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2616 653 5 %RANDOM
Rwork0.2167 ---
obs0.2189 12390 98.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.33 Å2 / Biso mean: 26.132 Å2 / Biso min: 16.61 Å2
Baniso -1Baniso -2Baniso -3
1-2.83 Å20 Å2-0 Å2
2---1.32 Å20 Å2
3----1.51 Å2
Refinement stepCycle: final / Resolution: 1.6→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms684 0 2 98 784
Biso mean--23.39 36.18 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0470.013727
X-RAY DIFFRACTIONr_bond_other_d0.0360.017681
X-RAY DIFFRACTIONr_angle_refined_deg2.2321.6491000
X-RAY DIFFRACTIONr_angle_other_deg2.3621.5611589
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4945100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.69620.825
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28115118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.047154
X-RAY DIFFRACTIONr_chiral_restr0.0640.2100
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02812
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02144
LS refinement shellResolution: 1.597→1.639 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 47 -
Rwork0.452 879 -
all-926 -
obs--95.96 %

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