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- PDB-1r4c: N-Truncated Human Cystatin C; Dimeric Form With 3D Domain Swapping -

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Basic information

Entry
Database: PDB / ID: 1r4c
TitleN-Truncated Human Cystatin C; Dimeric Form With 3D Domain Swapping
ComponentsCystatin C
KeywordsHYDROLASE INHIBITOR / HUMAN CYSTATIN C / N-TRUNCATION / 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: 2.18 Å
AuthorsJanowski, R. / Abrahamson, M. / Grubb, A. / Jaskolski, M.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Domain swapping in N-truncated human cystatin C.
Authors: Janowski, R. / 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: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression of a 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.
#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. / LeSauteur, L. / Gehring, K.
History
DepositionOct 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Cystatin C
D: Cystatin C
E: Cystatin C
F: Cystatin C
G: Cystatin C
H: Cystatin C


Theoretical massNumber of molelcules
Total (without water)98,7518
Polymers98,7518
Non-polymers00
Water3,693205
1
A: Cystatin C
B: Cystatin C


Theoretical massNumber of molelcules
Total (without water)24,6882
Polymers24,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5920 Å2
ΔGint-39 kcal/mol
Surface area13770 Å2
MethodPISA
2
C: Cystatin C
D: Cystatin C


Theoretical massNumber of molelcules
Total (without water)24,6882
Polymers24,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-42 kcal/mol
Surface area14000 Å2
MethodPISA
3
E: Cystatin C
F: Cystatin C


Theoretical massNumber of molelcules
Total (without water)24,6882
Polymers24,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-41 kcal/mol
Surface area13890 Å2
MethodPISA
4
G: Cystatin C
H: Cystatin C


Theoretical massNumber of molelcules
Total (without water)24,6882
Polymers24,6882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-40 kcal/mol
Surface area13920 Å2
MethodPISA
5
A: Cystatin C
B: Cystatin C
C: Cystatin C
D: Cystatin C

A: Cystatin C
B: Cystatin C
C: Cystatin C
D: Cystatin C


Theoretical massNumber of molelcules
Total (without water)98,7518
Polymers98,7518
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area38700 Å2
ΔGint-193 kcal/mol
Surface area40600 Å2
MethodPISA
6
E: Cystatin C
F: Cystatin C
G: Cystatin C
H: Cystatin C

E: Cystatin C
F: Cystatin C
G: Cystatin C
H: Cystatin C


Theoretical massNumber of molelcules
Total (without water)98,7518
Polymers98,7518
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area38250 Å2
ΔGint-195 kcal/mol
Surface area40970 Å2
MethodPISA
7
A: Cystatin C
B: Cystatin C

E: Cystatin C
F: Cystatin C


Theoretical massNumber of molelcules
Total (without water)49,3764
Polymers49,3764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455x-1/2,y+1/2,z1
Buried area13900 Å2
ΔGint-100 kcal/mol
Surface area25710 Å2
MethodPISA
8
C: Cystatin C
D: Cystatin C

G: Cystatin C
H: Cystatin C


Theoretical massNumber of molelcules
Total (without water)49,3764
Polymers49,3764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
Buried area13720 Å2
ΔGint-100 kcal/mol
Surface area25930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.147, 99.639, 206.066
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTHE EIGHT POLYPEPTIDE CHAINS ARE ASSEMBLED INTO 3D DOMAIN SWAPPED DIMERS IN THE FOLLOWING WAY: AB, CB, EF, GH

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Components

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


Mass: 12343.925 Da / Num. of mol.: 8 / Fragment: human cystatin C without 10 N-terminal residues
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


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: 0.4M (NH4)H2PO4, VAPOR DIFFUSION, HANGING DROP, temperature 292K, pH 8.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.104
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 24, 1999
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.104 Å / Relative weight: 1
ReflectionResolution: 2.18→25 Å / Num. obs: 52404 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 9.3 % / Biso Wilson estimate: 36.9 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.6
Reflection shellResolution: 2.18→2.26 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.126 / Mean I/σ(I) obs: 10.9 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN CYSTATIN C DIMER WITH SWAPPED DOMAINS (PDB ENTRY 1G96)

1g96


Resolution: 2.18→10 Å / SU B: 8.514 / SU ML: 0.226 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.284 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE REFINEMENT INCLUDED TLS PARAMETERS, HYDROGENS HAVE BEEN ADDED IN THE RIGID POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2632 5.1 %RANDOM
Rwork0.218 ---
obs0.22 51566 99.5 %-
all-51566 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.75 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å20 Å2
2---0.47 Å20 Å2
3----0.36 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21933 Å0.28385 Å
Refinement stepCycle: LAST / Resolution: 2.18→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 0 205 7117
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6351.937
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1020.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.9881.5
X-RAY DIFFRACTIONr_mcangle_it1.8492
X-RAY DIFFRACTIONr_scbond_it2.3813
X-RAY DIFFRACTIONr_scangle_it4.0964.5
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.802-0.58470.26590.6842-0.14550.4648-0.0252-0.0116-0.0307-0.02990.09710.0073-0.0362-0.0060.00670.0781-0.0010.0320.0778-0.02120.09183.813412.338812.7846
20.4035-0.30010.4550.53030.0220.7526-0.0740.08180.03670.07140.117-0.0601-0.05710.00940.00610.05340.00390.03760.0962-0.01110.08827.73998.514315.3265
31.2607-0.7461-0.62870.44790.38580.9341-0.06150.0017-0.0086-0.0143-0.0005-0.0020.04160.0527-0.06070.1136-0.01490.01230.05810.00750.0957.7762-15.52138.5673
41.3179-0.4522-0.7610.57650.13380.8333-0.04720.013-0.08220.0352-0.04460.02690.01260.0183-0.03930.074-0.0333-0.02910.07390.00620.05513.7328-12.667112.2501
51.30470.5938-0.4690.9080.15030.7212-0.0815-0.09250.0007-0.10120.0525-0.0422-0.0020.04160.09470.06620.0408-0.0560.08530.00770.076952.574-10.88437.7577
60.51690.50640.330.63110.42340.5723-0.0491-0.0303-0.0477-0.02560.02710.0255-0.0750.04720.05760.08780.0147-0.00290.09160.02230.099151.64614.88641.2682
70.7799-0.2563-0.25630.4005-0.07630.7171-0.03410.00540.0320.03850.04320.01410.0530.01940.02830.08340.046-0.02090.0713-0.00170.120548.401-14.44640.6937
80.59520.34920.45730.56760.29840.4859-0.0422-0.0112-0.0519-0.0496-0.00870.0067-0.02350.05190.05190.08480.01150.02290.11240.01960.097349.09911.31137.3525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 1201 - 110
2X-RAY DIFFRACTION2BB11 - 1201 - 110
3X-RAY DIFFRACTION3CC11 - 1201 - 110
4X-RAY DIFFRACTION4DD11 - 1201 - 110
5X-RAY DIFFRACTION5EE11 - 1201 - 110
6X-RAY DIFFRACTION6FF11 - 1201 - 110
7X-RAY DIFFRACTION7GG11 - 1201 - 110
8X-RAY DIFFRACTION8HH11 - 1201 - 110

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