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- PDB-3gax: Crystal structure of monomeric human cystatin C stabilized agains... -

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Basic information

Entry
Database: PDB / ID: 3gax
TitleCrystal structure of monomeric human cystatin C stabilized against aggregation
ComponentsCystatin-C
KeywordsHYDROLASE INHIBITOR / cysteine protease inhibitor / 3D domain swapping / protein aggregation / amyloid / protein engineering / twinning / Hereditary Cystatin C Amyloid Angiopathy / Amyloidosis / Disease mutation / Polymorphism / Protease inhibitor / Secreted / Thiol protease inhibitor
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: 1.7 Å
AuthorsKolodziejczyk, R. / Michalska, K. / Hernandez-Santoyo, A. / Wahlbom, M. / Grubb, A. / Jaskolski, M.
CitationJournal: Febs J. / Year: 2010
Title: Crystal structure of human cystatin C stabilized against amyloid formation.
Authors: Kolodziejczyk, R. / Michalska, K. / Hernandez-Santoyo, A. / Wahlbom, M. / Grubb, A. / Jaskolski, M.
History
DepositionFeb 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 6, 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

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Assembly

Deposited unit
A: Cystatin-C
B: Cystatin-C


Theoretical massNumber of molelcules
Total (without water)26,8022
Polymers26,8022
Non-polymers00
Water3,243180
1
A: Cystatin-C


Theoretical massNumber of molelcules
Total (without water)13,4011
Polymers13,4011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cystatin-C


Theoretical massNumber of molelcules
Total (without water)13,4011
Polymers13,4011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.260, 76.260, 97.576
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Cystatin-C / Cystatin-3 / Neuroendocrine basic polypeptide / Gamma-trace / Post-gamma-globulin


Mass: 13401.217 Da / Num. of mol.: 2 / Fragment: Human cystatin C stab1: UNP residues 27-146 / Mutation: L47C, G69C
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.: 180 / 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: 3.06 Å3/Da / Density % sol: 59.75 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.25M Ammonium phosphate, 150mM Sodium phosphate buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 7, 2008
Details: two mirrors and double crystal monochromator between them
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11h,k,l10.548
11-h-k,k,-l20.452
ReflectionResolution: 1.7→50 Å / Num. all: 35372 / Num. obs: 35237 / % possible obs: 99.8 % / Observed criterion σ(I): -2 / Redundancy: 10.5 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 25.9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.896 / Mean I/σ(I) obs: 2 / Num. unique all: 3444 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MAR345CCDdata collection
PHASERphasing
REFMAC5.5.0070refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G96

1g96


Resolution: 1.7→39.26 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / SU B: 3.754 / SU ML: 0.048 / Cross valid method: FREE R / σ(F): 0 / ESU R: 0.014 / ESU R Free: 0.015 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1672 1037 2.9 %random, including twin-law related pairs
Rwork0.13842 ---
all0.13926 35237 --
obs0.13926 35237 99.65 %-
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: 10.838 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å20 Å20 Å2
2--3.28 Å20 Å2
3----6.55 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 0 180 1869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211905
X-RAY DIFFRACTIONr_bond_other_d0.0010.021317
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.9252608
X-RAY DIFFRACTIONr_angle_other_deg0.9383.0083180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4185252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0123.36798
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.52715319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2211517
X-RAY DIFFRACTIONr_chiral_restr0.1070.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212226
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02417
X-RAY DIFFRACTIONr_mcbond_it1.0271.51171
X-RAY DIFFRACTIONr_mcbond_other0.3371.5461
X-RAY DIFFRACTIONr_mcangle_it1.66721911
X-RAY DIFFRACTIONr_scbond_it2.53734
X-RAY DIFFRACTIONr_scangle_it3.7214.5688
LS refinement shellResolution: 1.7→1.792 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.26 159 -
Rwork0.218 4847 -
obs-4847 97.74 %
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)
15.0654-0.26421.3336.04912.64438.4969-0.07210.4438-0.475-0.35390.1506-0.11730.51460.0848-0.07840.2501-0.0820.02330.2762-0.02620.1007-19.879432.234551.3587
24.34441.73331.67585.84184.442210.825-0.1356-0.03980.1899-0.1416-0.08330.2235-0.3442-0.41680.21890.157-0.00750.00710.1720.03990.087-20.516442.705662.8968
33.9831.6943-0.27965.11851.3072.34670.01120.13270.0137-0.13690.1131-0.18240.0014-0.049-0.12440.1859-0.0174-0.02070.20970.04640.0425-14.829841.024661.39
44.19944.28230.4376.90091.46321.98120.02470.0650.0217-0.07730.0670.0209-0.1081-0.0796-0.09160.2287-0.0075-0.00040.24280.02820.057-14.409941.240261.4303
51.21582.0556-1.01473.5321-1.25864.55060.21930.67921.0837-0.5322-0.0471.3998-0.9271-1.1516-0.17220.34380.13020.00670.39870.06230.4272-18.145656.656261.6604
63.70373.5443-1.04447.18870.24044.67950.16210.05910.0813-0.062-0.0242-0.4568-0.38660.1725-0.13790.2141-0.05670.04690.1925-0.01750.06-3.299550.240363.7194
711.38862.48854.39252.98671.37473.5834-0.1665-0.11460.0609-0.17260.01040.4247-0.0805-0.35650.15620.1798-0.02-0.02130.190.00780.0998-26.293233.211562.334
820.1543.63193.72364.57871.18444.7666-0.1675-0.17540.09280.00710.1133-0.3136-0.15730.21610.05410.1723-0.0134-0.02090.15490.00240.0278-11.099836.240368.1399
96.699-0.1787-3.27795.4925-0.83858.4719-0.0178-0.30320.24760.218-0.0508-0.49480.00270.38820.06860.3494-0.0124-0.04430.18880.01770.12161.312863.105659.5612
103.9672.38682.81917.71542.9856.2799-0.13050.02590.2559-0.104-0.0550.4944-0.2008-0.44730.18540.19530.00110.02790.17480.04570.0705-9.566960.64647.7792
114.07332.38161.44115.9620.96533.39420.1573-0.0969-0.24490.1379-0.0106-0.01430.1548-0.2408-0.14660.2256-0.01740.02840.17020.02660.0656-7.098852.919748.5409
125.30041.16881.279413.05631.58294.1861-0.1060.02720.48430.07770.0733-0.5504-0.66390.31990.03270.3241-0.06020.00970.16530.01180.11012.28168.920151.0423
137.8585.51024.03878.12732.62343.86460.193-0.0682-0.34480.12230.0378-0.10060.2564-0.15-0.23070.2427-0.03850.00280.16940.02550.0989-7.627948.575147.8055
140.1753-1.22890.02118.6183-0.17690.4134-0.0314-0.15850.13830.822-0.08510.627-0.4798-0.36280.11640.55670.1376-0.10330.542-0.02380.2868-20.302150.436547.6324
155.09413.0953-0.33077.7562-0.53242.33690.1841-0.0271-0.965-0.1458-0.0388-0.46140.4507-0.2754-0.14530.2501-0.0451-0.06190.13560.02760.1845-6.820742.423845.6956
163.74111.38450.09499.99091.80162.6605-0.0005-0.0290.1976-0.1927-0.0547-0.0175-0.2497-0.10960.05520.2562-0.00160.00530.1780.00480.0374-2.514964.874945.4596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 23
2X-RAY DIFFRACTION2A24 - 37
3X-RAY DIFFRACTION3A38 - 58
4X-RAY DIFFRACTION4A59 - 74
5X-RAY DIFFRACTION5A75 - 82
6X-RAY DIFFRACTION6A83 - 96
7X-RAY DIFFRACTION7A97 - 111
8X-RAY DIFFRACTION8A112 - 120
9X-RAY DIFFRACTION9B12 - 20
10X-RAY DIFFRACTION10B21 - 38
11X-RAY DIFFRACTION11B39 - 54
12X-RAY DIFFRACTION12B55 - 64
13X-RAY DIFFRACTION13B65 - 72
14X-RAY DIFFRACTION14B73 - 84
15X-RAY DIFFRACTION15B85 - 97
16X-RAY DIFFRACTION16B98 - 120

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