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- PDB-1g96: HUMAN CYSTATIN C; DIMERIC FORM WITH 3D DOMAIN SWAPPING -

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Basic information

Entry
Database: PDB / ID: 1g96
TitleHUMAN CYSTATIN C; DIMERIC FORM WITH 3D DOMAIN SWAPPING
ComponentsCYSTATIN C
Keywordshydrolase inhibitor / human cystatin C dimer / 3D domain swapping / amyloid formation / inhibitor of C1 and C13 cysteine proteases / AMYLOID ANGIOPATHY AND 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: 2.5 Å
AuthorsJanowski, R. / Kozak, M. / Jankowska, E. / Grzonka, Z. / Grubb, A. / Abrahamson, M. / Jaskolski, M.
Citation
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.
#1: 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.
#2: Journal: Embo J. / Year: 1988
Title: The 2.0 angstrom X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteases
Authors: Bode, W. / Engh, R. / Musil, D. / Thiele, U. / Huber, R. / Karshikov, A. / Brzin, J. / Kos, J. / Turk, V.
#3: 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
DepositionNov 22, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYSTATIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4933
Polymers13,3651
Non-polymers1282
Water39622
1
A: CYSTATIN C
hetero molecules

A: CYSTATIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9856
Polymers26,7302
Non-polymers2554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area6420 Å2
ΔGint-38 kcal/mol
Surface area13750 Å2
MethodPISA
2
A: CYSTATIN C
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)107,94224
Polymers106,9218
Non-polymers1,02016
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_655-x+1,z,y1
crystal symmetry operation19_655-x+1,-z,-y1
crystal symmetry operation20_555x,-z,y1
Buried area40850 Å2
ΔGint-176 kcal/mol
Surface area39830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.53, 140.53, 140.53
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Cell settingcubic
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-301-

CL

DetailsHuman cystatin C in the present structure forms crystallographic dimers with 3D swapped domains. The dimer is generated by two-fold rotation of the 4(2) axis using the following transformation: 1/2-x, -y, z.

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Components

#1: Protein CYSTATIN C / GAMMA-TRACE / POST-GAMMA-GLOBULIN


Mass: 13365.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHD 313 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P01034
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / 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: 4.3 Å3/Da / Density % sol: 71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: Lyophilized protein was dissolved in 100 mM sodium acetate buffer pH 4.8 containing 20 mM CaCl2. Droplets were equilibrated against 1 ml of reservoir with analogous buffer/CaCl2 solution. ...Details: Lyophilized protein was dissolved in 100 mM sodium acetate buffer pH 4.8 containing 20 mM CaCl2. Droplets were equilibrated against 1 ml of reservoir with analogous buffer/CaCl2 solution. After 2 and 4 days, the reservoir solution was supplemented with 100 microliters of MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mMsodium acetate1drop
320 mM1dropCaCl2
4MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8423 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2000
RadiationMonochromator: monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8423 Å / Relative weight: 1
ReflectionResolution: 2.5→40 Å / Num. all: 8429 / Num. obs: 8429 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.9 % / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 2.5 / % possible all: 93.5
Reflection
*PLUS
Num. measured all: 167936
Reflection shell
*PLUS
% possible obs: 93.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-terminally truncated chicken cystatin (1cew.pdb) converted to a polyalanine chain and limited to those fragments that had been modeled in electron density (residues 86-90 not included)

1cew


Resolution: 2.5→20 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: individual isotropic / Cross valid method: free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.249 815 9.6 %random
Rwork0.22 ---
all0.216 8500 --
obs0.216 8429 99.2 %-
Solvent computationSolvent model: flat model / Bsol: 38.73 Å2 / ksol: 0.33 e/Å3
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 7 22 900
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d1.85
X-RAY DIFFRACTIONc_mcbond_it2.411.5
X-RAY DIFFRACTIONc_mcangle_it4.032
X-RAY DIFFRACTIONc_scbond_it3.92
X-RAY DIFFRACTIONc_scangle_it6.082.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.331 70 8.3 %
Rwork0.328 714 -
obs-784 93.5 %
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.85

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