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- PDB-1tij: 3D Domain-swapped human cystatin C with amyloid-like intermolecul... -

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Basic information

Entry
Database: PDB / ID: 1tij
Title3D Domain-swapped human cystatin C with amyloid-like intermolecular beta-sheets
ComponentsCystatin C
KeywordsHYDROLASE INHIBITOR / HUMAN CYSTATIN C DIMER / 3D DOMAIN SWAPPING / AMYLOID FORMATION / INHIBITOR OF C1 AND C13 CYSTEINE PROTEASES / AMYLOID ANGIOPATHY / CEREBRAL HEMORRHAGE
Function / homology
Function and homology information


negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization ...negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / negative regulation of peptidase activity / peptidase inhibitor activity / negative regulation of extracellular matrix disassembly / regulation of tissue remodeling / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / supramolecular fiber organization / negative regulation of proteolysis / Post-translational protein phosphorylation / defense response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / tertiary granule lumen / amyloid-beta binding / protease binding / vesicle / ficolin-1-rich granule lumen / Amyloid fiber formation / endoplasmic reticulum lumen / Neutrophil degranulation / Golgi apparatus / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
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: 3.03 Å
AuthorsJanowski, R. / Kozak, M. / Abrahamson, M. / Grubb, A. / Jaskolski, M.
Citation
Journal: Proteins / Year: 2005
Title: 3D domain-swapped human cystatin C with amyloidlike intermolecular beta-sheets.
Authors: Janowski, R. / Kozak, M. / Abrahamson, M. / Grubb, A. / Jaskolski, M.
#1: Journal: Nat.Struct.Biol. / Year: 2001
Title: Human cystatin C, an amyloidogenic protein, dimerizes through three-dimensional domain swapping
Authors: Janowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Grubb, A. / Abrahamson, M. / Jaskolski, M.
#2: Journal: To be Published
Title: 3D domain swapping in n-truncated human cystatin C
Authors: Janowski, R. / Abrahamson, M. / Grubb, A. / Jaskolski, M.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression of selenomethionyl derivative and preliminary crystallographic studies of human cystatin C
Authors: Kozak, M. / Jankowska, E. / Janowski, R. / Grzonka, Z. / Grubb, A. / Alvarez Fernandez, M. / Abrahamson, M. / Jaskolski, M.
#4: Journal: J.Mol.Biol. / Year: 1997
Title: NMR structural studies of human cystatin C dimers and monomers
Authors: Ekiel, I. / Abrahamson, M. / Fulton, D.B. / Lindahl, P. / Storer, A.C. / Levadoux, W. / Lafrance, M. / Labelle, S. / Pomerleau, Y. / Groleau, D. / Lesauter, L. / Gehring, K.
History
DepositionJun 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAINS INTERTWINED TO FORM A 3D DOMAIN SWAPPED DIMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cystatin C
B: Cystatin C


Theoretical massNumber of molelcules
Total (without water)26,7302
Polymers26,7302
Non-polymers00
Water39622
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-39.2 kcal/mol
Surface area13360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.49, 91.49, 144.45
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212
DetailsTHIS ENTRY CORRESPONDS TO THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF TWO CHAINS, A AND B, INTERTWINED INTO A 3D DOMAIN-SWAPPED DIMER

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Components

#1: Protein Cystatin C / / Gamma-trace / Post-gamma-globulin


Mass: 13365.141 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CST3 / Plasmid: PHD 313 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P01034
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 5.6 Å3/Da / Density % sol: 77.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100mM sodium acetate, 20mM CaCl2, 40-45% MPD, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8885 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 10, 1996 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8885 Å / Relative weight: 1
ReflectionResolution: 3.03→40 Å / Num. all: 12273 / Num. obs: 12273 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 57.9 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 14
Reflection shellResolution: 3.03→3.08 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 3.2 / Num. unique all: 599 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ONE HALF OF HUMAN CYSTATIN C CRYSTALLOGRAPHIC DIMER WITH SWAPPED DOMAINS (PDB ENTRY 1G96)

1g96


Resolution: 3.03→15 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 77294.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: Bulk solvent correction used
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1070 9 %RANDOM
Rwork0.217 ---
all0.223 11902 --
obs0.217 11902 96.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 26.969 Å2 / ksol: 0.271825 e/Å3
Displacement parametersBiso mean: 42.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.32 Å20 Å20 Å2
2--4.32 Å20 Å2
3----8.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.62 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3.03→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1776 0 0 22 1798
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.2
LS refinement shellResolution: 3.03→3.22 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.347 157 8.2 %
Rwork0.31 1754 -
obs-1754 95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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