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- PDB-3nx0: Hinge-loop mutation can be used to control 3D domain swapping and... -

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Basic information

Entry
Database: PDB / ID: 3nx0
TitleHinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C
ComponentsCystatin-C
KeywordsHYDROLASE INHIBITOR / cysteine protease inhibitor / 3D domain swapping / protein engineering / protein oligomerization / protein aggregation / amyloid
Function / homology
Function and homology information


negative regulation of collagen catabolic process / negative regulation of elastin catabolic process / negative regulation of blood vessel remodeling / peptidase inhibitor activity / negative regulation of peptidase 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 / peptidase inhibitor activity / negative regulation of peptidase 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: 2.04 Å
AuthorsOrlikowska, M. / Jankowska, E. / Kolodziejczyk, R. / Jaskolski, M. / Szymanska, A.
CitationJournal: J.Struct.Biol. / Year: 2011
Title: Hinge-loop mutation can be used to control 3D domain swapping and amyloidogenesis of human cystatin C.
Authors: Orlikowska, M. / Jankowska, E. / Kolodziejczyk, R. / Jaskolski, M. / Szymanska, A.
History
DepositionJul 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9524
Polymers26,7602
Non-polymers1922
Water3,117173
1
A: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4762
Polymers13,3801
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4762
Polymers13,3801
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.316, 76.316, 97.723
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: 13380.112 Da / Num. of mol.: 2 / Fragment: UNP residues 27-146 / Mutation: V57N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CST3 / Plasmid: pHD313 / Production host: Escherichia coli (E. coli) / Strain (production host): C41(DE3) / References: UniProt: P01034
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Compound detailsAUTHORS STATE THAT THE CHIRALITY CHANGE AT CA ATOM OF ASN A57 IS CAUSED BY AN INTERMOLECULAR ...AUTHORS STATE THAT THE CHIRALITY CHANGE AT CA ATOM OF ASN A57 IS CAUSED BY AN INTERMOLECULAR HYDROGEN BOND WITH H90 RESIDUE FROM A MOLECULE RELATED BY CRYSTALLOGRAPHIC SYMMETRY. THIS INTERACTION BETWEEN THE CARBONYL O ATOM OF N57 AND THE N ATOM OF H90 MAY ADDITIONALLY FORCE THE ASPARAGINE TO ADOPT THE STRAINED CONFORMATION.

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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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M sodium cacodylate, 0.2 M ammonium sulfate and 25% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.81272 Å
DetectorDetector: CCD / Date: Nov 28, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81272 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. obs: 20617 / % possible obs: 95.8 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 20.5
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1451 / % possible all: 71.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.04→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.05 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22474 998 5.1 %RANDOM
Rwork0.17899 ---
obs0.18137 18703 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.21 Å2
Refinement stepCycle: LAST / Resolution: 2.04→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1722 0 10 173 1905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0221809
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8361.9452455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7725226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.22223.54893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78915309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5831517
X-RAY DIFFRACTIONr_chiral_restr0.2480.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211407
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_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.931.51103
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.59321780
X-RAY DIFFRACTIONr_scbond_it2.8233706
X-RAY DIFFRACTIONr_scangle_it4.5514.5670
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 39 -
Rwork0.254 989 -
obs--68.9 %
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)
15.27143.1293-4.62833.2599-1.05211.8446-0.1207-0.9599-0.35240.1860.1923-0.2801-0.06760.6391-0.07170.2386-0.0561-0.03390.4970.03330.238220.5421-33.021712.1677
210.18770.4146.53792.3908-0.970510.2535-0.0523-0.30110.3270.08760.03690.0984-0.7248-0.31610.01530.1529-0.0260.05240.1452-0.02220.184612.4608-26.89441.8019
340.34323.0367-6.39457.05351.88.5478-0.21431.32260.872-0.26860.22690.0097-0.5567-0.1665-0.01260.1844-0.02220.01960.25570.12260.10783.6106-27.779-10.3127
47.30370.81773.0541.84190.12212.99630.0971-0.2666-0.33830.14850.0216-0.1385-0.0252-0.0334-0.11860.1252-0.02320.02660.1999-0.0450.132614.3062-33.14224.4504
58.6084-0.10051.35471.15640.292.75060.11410.03870.01530.0964-0.01370.0554-0.1933-0.0786-0.10040.1168-0.00880.04810.13350.00680.08759.2076-32.10090.8191
67.42050.9339-2.01734.24142.172414.19550.3132-0.26590.83590.00780.10230.6291-1.4176-0.198-0.41560.19860.09310.09380.25040.00850.2143-4.3646-29.11531.4505
717.20982.62433.02732.144-0.61352.48130.3435-0.3967-0.77380.006-0.0555-0.0570.093-0.1662-0.28790.14780.0167-0.00320.1766-0.00750.12624.0434-38.9106-2.3511
87.46356.38695.33289.13235.40676.0007-0.21270.0922-0.1117-0.28570.157-0.0873-0.2910.24890.05570.1174-0.03580.03380.1881-0.02550.110919.8188-29.5714-1.6696
96.4813.2241-4.46468.0506-2.179713.8261-0.36941.2193-0.0337-0.41840.76820.63360.0659-0.7834-0.39890.13660.1241-0.0420.4619-0.03720.2327-17.9772-34.26064.0872
1014.1233-1.54416.56890.71180.26257.14910.0821-0.29180.5955-0.07760.0433-0.1074-0.62950.0133-0.12530.17210.00530.07240.1739-0.01670.2043-8.2921-27.592417.2043
118.1989-0.53611.34181.5504-0.35652.32930.25620.397-0.2204-0.1446-0.05960.0168-0.0519-0.064-0.19660.09310.04140.02730.22020.0090.1162-10.6309-33.637212.3072
127.4843-0.1194-0.16140.7727-0.35591.78940.10950.2089-0.1523-0.0990.0238-0.0333-0.3107-0.0838-0.13330.14340.0190.03510.1822-0.01290.1231-7.1508-33.235414.626
139.3657-3.12419.5133-3.089-2.598134.055-0.11890.63160.234-0.0348-0.05620.058-1.37111.62220.17510.7108-0.23640.04460.4872-0.08370.60263.3042-21.975514.4291
143.4464.6729-3.4895.7947-4.749813.47030.1149-0.0402-0.40760.11940.0021-0.4950.05480.5927-0.1170.0847-0.0423-0.00840.2492-0.03070.2778.78-35.776216.2318
158.1299-3.56861.9953.6285-1.14972.2184-0.0343-0.2153-0.56960.03720.13130.3436-0.2311-0.1891-0.0970.15160.00480.01290.203-0.02230.1176-12.9515-33.138715.9386
168.7324-6.10091.0049.7801-1.45383.9249-0.18-0.1327-0.16640.298-0.01530.0012-0.0797-0.28620.19530.13390.01690.01870.1899-0.0010.0828-14.2621-32.588519.6654
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 21
2X-RAY DIFFRACTION2A22 - 35
3X-RAY DIFFRACTION3A36 - 41
4X-RAY DIFFRACTION4A42 - 59
5X-RAY DIFFRACTION5A60 - 75
6X-RAY DIFFRACTION6A76 - 89
7X-RAY DIFFRACTION7A90 - 99
8X-RAY DIFFRACTION8A100 - 120
9X-RAY DIFFRACTION9B11 - 21
10X-RAY DIFFRACTION10B22 - 40
11X-RAY DIFFRACTION11B41 - 59
12X-RAY DIFFRACTION12B60 - 74
13X-RAY DIFFRACTION13B75 - 82
14X-RAY DIFFRACTION14B83 - 91
15X-RAY DIFFRACTION15B92 - 106
16X-RAY DIFFRACTION16B107 - 120

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