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- PDB-2oct: Stefin B (Cystatin B) tetramer -

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Basic information

Entry
Database: PDB / ID: 2oct
TitleStefin B (Cystatin B) tetramer
ComponentsCystatin B
KeywordsPROTEIN BINDING / stefin / cystatin / amyloid / domain-swapping / hand shaking / proline isomerization
Function / homology
Function and homology information


negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / adult locomotory behavior / negative regulation of proteolysis / tertiary granule lumen / secretory granule lumen / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen ...negative regulation of peptidase activity / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / adult locomotory behavior / negative regulation of proteolysis / tertiary granule lumen / secretory granule lumen / collagen-containing extracellular matrix / protease binding / ficolin-1-rich granule lumen / Neutrophil degranulation / nucleolus / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleus / cytoplasm / cytosol
Similarity search - Function
Proteinase inhibitor I25A, stefin / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsJenko Kokalj, S. / Guncar, G. / Turk, D.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Essential role of proline isomerization in stefin B tetramer formation.
Authors: Jenko Kokalj, S. / Guncar, G. / Stern, I. / Morgan, G. / Rabzelj, S. / Kenig, M. / Staniforth, R.A. / Waltho, J.P. / Zerovnik, E. / Turk, D.
History
DepositionDec 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Cystatin B
B: Cystatin B


Theoretical massNumber of molelcules
Total (without water)22,3272
Polymers22,3272
Non-polymers00
Water3,099172
1
A: Cystatin B
B: Cystatin B

A: Cystatin B
B: Cystatin B


Theoretical massNumber of molelcules
Total (without water)44,6544
Polymers44,6544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area11350 Å2
ΔGint-84 kcal/mol
Surface area19870 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)120.123, 30.857, 51.349
Angle α, β, γ (deg.)90.00, 95.81, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe second part of the biological assembly is generated by the two fold axis: -x, y, -z+1.

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Components

#1: Protein Cystatin B / Liver thiol proteinase inhibitor / CPI-B / Stefin B


Mass: 11163.533 Da / Num. of mol.: 2 / Mutation: C3S, P79S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSTB / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P04080
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.12 Å3/Da / Density % sol: 41.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 30 % MPD, 0.1 M HEPES, 1.4-butanediol as additive, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→100 Å / Num. obs: 37806 / Rmerge(I) obs: 0.11
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.587 / Num. unique all: 3709 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1STF

1stf


Resolution: 1.4→10 Å / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.189 1818 RANDOM
Rwork0.176 --
obs0.18 35894 -
all-75962 -
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 0 172 1718
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0145
X-RAY DIFFRACTIONc_angle_deg2.28

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