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- PDB-6ztk: Crystal structure of Mialostatin, a gut cystatin from the hard ti... -

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Basic information

Entry
Database: PDB / ID: 6ztk
TitleCrystal structure of Mialostatin, a gut cystatin from the hard tick Ixodes ricinus
ComponentsMialostatin
KeywordsPROTEIN BINDING / cystatin / protease inhibitor / ixodes ricinus / tick / hydrolase inhibitor
Function / homologyCystatin domain / Cystatin-like domain / Cystatin domain / cysteine-type endopeptidase inhibitor activity / Putative tick cistatins 1
Function and homology information
Biological speciesIxodes ricinus (castor bean tick)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsBusa, M. / Rezacova, P. / Mares, M.
Funding supportEuropean Union, Czech Republic, 2items
OrganizationGrant numberCountry
European Regional Development FundCZ.02.1.01/0.0/0.0/16_019/0000729European Union
Ministry of Education (MoE, Czech Republic)61388963 Czech Republic
CitationJournal: Int J Mol Sci / Year: 2021
Title: Mialostatin, a Novel Midgut Cystatin from Ixodes ricinus Ticks: Crystal Structure and Regulation of Host Blood Digestion.
Authors: Kotal, J. / Busa, M. / Urbanova, V. / Rezacova, P. / Chmelar, J. / Langhansova, H. / Sojka, D. / Mares, M. / Kotsyfakis, M.
History
DepositionJul 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Mialostatin
A: Mialostatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5317
Polymers31,5382
Non-polymers9935
Water6,648369
1
B: Mialostatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2183
Polymers15,7691
Non-polymers4492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Mialostatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3144
Polymers15,7691
Non-polymers5453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.106, 81.106, 162.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-475-

HOH

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Components

#1: Protein Mialostatin / Mialostatin


Mass: 15768.985 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Mialostatin / Source: (gene. exp.) Ixodes ricinus (castor bean tick) / Production host: Escherichia coli (E. coli) / References: UniProt: V5H924
#2: Chemical ChemComp-TRT / FRAGMENT OF TRITON X-100 / 1-{2-[2-(2-METHOXYETHOXY)ETHOXY]ETHOXY}-4-(1,1,3,3-TETRAMETHYLBUTYL)BENZENE / Triton X-100


Mass: 352.508 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36O4 / Comment: detergent*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.61 % / Description: hexagonal prism
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 1M ammonium sulphate 0.1M sodium citrate pH 4.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.55→42.9 Å / Num. obs: 46381 / % possible obs: 99.9 % / Redundancy: 21.22 % / Biso Wilson estimate: 19.54 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.08446 / Rpim(I) all: 0.01874 / Rrim(I) all: 0.087 / Net I/av σ(I): 17.13 / Net I/σ(I): 21.95
Reflection shellResolution: 1.55→1.65 Å / Redundancy: 21.55 % / Rmerge(I) obs: 1.203 / Mean I/σ(I) obs: 2 / Num. unique obs: 4528 / CC1/2: 0.764 / CC star: 0.936 / Rpim(I) all: 0.263 / Rrim(I) all: 1.232 / % possible all: 99.25

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0R

3l0r


Resolution: 1.55→42.9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.266 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.068 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2014 2328 5 %RANDOM
Rwork0.1707 ---
obs0.1722 44052 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.8 Å2 / Biso mean: 20.97 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å2-0 Å2
3---0.13 Å2
Refinement stepCycle: final / Resolution: 1.55→42.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1737 0 63 371 2171
Biso mean--42.48 37.47 -
Num. residues----218
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0131923
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171745
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.6652646
X-RAY DIFFRACTIONr_angle_other_deg1.541.5684078
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3895241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.58524.25594
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.40215317
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.207157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022113
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02372
LS refinement shellResolution: 1.552→1.592 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 178 -
Rwork0.227 3183 -
all-3361 -
obs--98.91 %

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