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- PDB-3ps8: Crystal structure of L68V mutant of human cystatin C -

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Basic information

Entry
Database: PDB / ID: 3ps8
TitleCrystal structure of L68V mutant of human cystatin C
ComponentsCystatin-C
KeywordsHYDROLASE INHIBITOR / cysteine protease inhibitor / 3D domain swapping / Hereditary Cystatin C Amyloid Angiopathy / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Cystatin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsOrlikowska, M. / Borek, D. / Otwinowski, Z. / Skowron, P. / Szymanska, A.
CitationJournal: To be Published
Title: Crystal structure of L68V mutant of human cystatin C
Authors: Orlikowska, M. / Szymanska, A. / Borek, D. / Otwinowski, Z. / Skowron, P. / Jankowska, E.
History
DepositionDec 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)13,7295
Polymers13,3511
Non-polymers3774
Water1,44180
1
A: Cystatin-C
hetero molecules

A: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,45710
Polymers26,7022
Non-polymers7558
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area7530 Å2
ΔGint-34 kcal/mol
Surface area14030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.801, 139.801, 139.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-204-

HOH

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Components

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


Mass: 13351.114 Da / Num. of mol.: 1 / Mutation: L68V
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 / References: UniProt: P01034
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 4.26 Å3/Da / Density % sol: 71.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M sodium acetate pH=4.6, 8% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 7932 / Num. obs: 7932 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 42.9 % / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 41.57
Reflection shellResolution: 2.55→2.59 Å / Redundancy: 41.9 % / Mean I/σ(I) obs: 2.23

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→33 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.891 / SU B: 15.921 / SU ML: 0.162 / Cross valid method: THROUGHOUT / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25055 356 4.8 %RANDOM
Rwork0.18769 ---
obs0.19069 7087 94.01 %-
all-7932 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.265 Å2
Refinement stepCycle: LAST / Resolution: 2.55→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms859 0 25 80 964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022900
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9531209
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9215108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.34523.86444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.95615146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.817157
X-RAY DIFFRACTIONr_chiral_restr0.110.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021686
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_it3.9671.5547
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.4712879
X-RAY DIFFRACTIONr_scbond_it12.7443353
X-RAY DIFFRACTIONr_scangle_it15.7694.5330
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.55→2.617 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 30 -
Rwork0.245 405 -
obs--76.18 %
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)
14.3944-9.6954-4.836633.42463.525818.0301-0.9857-1.1616-0.05762.27650.61860.3608-0.00221.49230.36710.22890.1488-0.03060.73930.08510.139686.6852-5.222431.1056
243.1899-15.432129.630525.11724.388249.29170.4711-1.9287-2.96281.82880.1078-0.20133.3855-0.5387-0.57890.53360.10370.07240.35460.25440.450481.8861-15.387528.8665
37.6345-4.7349-4.58962.8193.915126.7931-0.2962-0.2096-0.37280.0705-0.0143-0.01570.55260.19220.31050.13550.05690.09280.08450.06440.150980.0893-13.146116.0757
42.52470.42371.92424.21828.031114.9588-0.2247-0.2456-0.23740.14570.19280.0050.2080.19920.03190.16720.01760.08120.09370.09110.170586.4009-13.947312.2409
519.4764-7.91676.51353.4547-1.6245.3809-0.3084-0.46720.31850.08290.1699-0.1504-0.07880.04820.13860.10630.0290.00550.15790.060.064867.16252.404827.2229
69.60983.4751-2.62978.4948-13.093719.8134-0.0248-0.70490.6190.27030.0330.3097-0.2002-0.1164-0.00820.17950.1227-0.0290.1437-0.0970.221249.940717.06179.0394
7-0.45710.09957.82416.0574-8.60258.1252-0.3453-0.22750.73052.66240.197-0.1747-2.05120.49390.14830.7836-0.0271-0.14240.505-0.56970.917655.93125.552410.5065
821.34443.27189.68958.727515.265436.6559-0.40820.89370.4612-0.8045-0.21541.1378-1.0505-2.00780.62360.2240.0357-0.11660.36560.16160.324744.111418.44183.3874
99.7381-2.59266.73445.8239-3.464110.3461-0.09450.0397-0.0275-0.15070.05330.4569-0.0842-0.23660.04130.07390.0527-0.01040.1107-0.02550.063455.45496.747316.2705
1013.68825.9798-11.355782.306-2.23649.81290.4008-1.7054-0.04011.7115-0.5261-4.0397-0.48282.30630.12530.3620.0401-0.29510.6846-0.14140.496572.664610.26929.3744
1121.18395.460910.93069.44364.972711.885-0.41150.59570.0785-0.52940.22280.3159-0.28020.13930.18870.15580.05250.03870.12980.02380.041258.56154.998215.1253
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A12 - 18
2X-RAY DIFFRACTION2A19 - 25
3X-RAY DIFFRACTION3A26 - 35
4X-RAY DIFFRACTION4A36 - 52
5X-RAY DIFFRACTION5A53 - 66
6X-RAY DIFFRACTION6A67 - 73
7X-RAY DIFFRACTION7A74 - 83
8X-RAY DIFFRACTION8A84 - 92
9X-RAY DIFFRACTION9A93 - 103
10X-RAY DIFFRACTION10A104 - 108
11X-RAY DIFFRACTION11A109 - 120

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