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- PDB-3s67: Crystal structure of V57P mutant of human cystatin C -

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Basic information

Entry
Database: PDB / ID: 3s67
TitleCrystal structure of V57P mutant of human cystatin C
ComponentsCystatin-C
KeywordsHYDROLASE 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 / IMIDAZOLE / DI(HYDROXYETHYL)ETHER / Cystatin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsOrlikowska, M. / Szymanska, A. / Borek, D. / Otwinowski, Z. / Skowron, P. / Jankowska, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Structural characterization of V57D and V57P mutants of human cystatin C, an amyloidogenic protein.
Authors: Orlikowska, M. / Szymanska, A. / Borek, D. / Otwinowski, Z. / Skowron, P. / Jankowska, E.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 27, 2013Group: Derived calculations
Revision 1.2Apr 3, 2013Group: Database references
Revision 1.3Sep 13, 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 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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)14,03210
Polymers13,3631
Non-polymers6699
Water1,20767
1
A: Cystatin-C
hetero molecules

A: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,06420
Polymers26,7262
Non-polymers1,33818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)140.135, 140.135, 140.135
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-124-

IMD

21A-125-

IMD

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 13363.124 Da / Num. of mol.: 1 / Mutation: V57P
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

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Non-polymers , 5 types, 76 molecules

#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 4.29 Å3/Da / Density % sol: 71.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Imidazole pH=6.5 0.9M Sodium acetate, additive 2.0M NDSB-221, 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: 0.97923 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 11234 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 14 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 36.5
Reflection shellResolution: 2.26→2.3 Å / Redundancy: 12.5 % / Mean I/σ(I) obs: 2.16

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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
Starting model: PDB ENTRY 1G96

1g96


Resolution: 2.26→27.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.08 / SU ML: 0.104 / Cross valid method: THROUGHOUT / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2289 537 4.8 %RANDOM
Rwork0.18667 ---
obs0.18869 10697 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.279 Å2
Refinement stepCycle: LAST / Resolution: 2.26→27.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms871 0 44 67 982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022929
X-RAY DIFFRACTIONr_bond_other_d0.0010.023
X-RAY DIFFRACTIONr_angle_refined_deg1.6571.9731243
X-RAY DIFFRACTIONr_angle_other_deg0.32336
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775110
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.88223.86444
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2315147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.564157
X-RAY DIFFRACTIONr_chiral_restr0.1160.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021716
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_it3.8151.5563
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.1872898
X-RAY DIFFRACTIONr_scbond_it9.6893366
X-RAY DIFFRACTIONr_scangle_it12.6024.5345
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.26→2.322 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 43 -
Rwork0.279 774 -
obs--99.76 %
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)
19.8423-4.32983.708947.8849-3.234613.1069-0.22290.29071.06223.1208-0.068-0.5079-1.25561.94810.2910.3541-0.1079-0.0310.33320.0530.214286.2928-1.101231.9856
233.20989.823114.591811.3053-1.419737.84720.5404-0.0766-1.80050.618-0.3681-0.52023.00641.3054-0.17230.52390.13420.01770.1612-0.00780.264283.3255-15.378629.2776
32.2045-0.8076-2.48093.87317.955519.8714-0.11630.0864-0.01310.01-0.30130.3458-0.0309-0.64580.41760.11990.02530.00660.1693-0.00830.225679.8345-14.484312.326
41.38790.1541-0.193311.476111.469812.81230.1434-0.3069-0.03310.52850.6693-0.98520.50360.4885-0.81270.15840.0642-0.01840.2061-0.05130.232689.9975-13.129317.4707
56.2909-2.19120.93581.4820.09040.9303-0.04340.06340.13960.0899-0.0007-0.06360.02320.13440.04410.16180.02520.00870.13080.02640.160470.81041.521528.619
61.8788-0.80660.406112.7665-16.651723.5324-0.16020.1219-0.3498-0.18620.50380.23890.322-0.6883-0.34360.13940.0257-0.03790.208-0.01240.328850.510711.278313.2768
77.97414.2991.90633.58160.816412.66190.05260.00640.7055-0.04620.22090.1808-0.93680.412-0.27340.2077-0.0225-0.01570.15770.00610.155656.108223.9256.4092
821.95036.1527-2.618112.5288-1.713814.70070.548-0.93721.46971.1572-0.22830.983-0.7387-0.5554-0.31980.25170.10520.05990.1636-0.02910.27650.609923.843910.9942
917.65281.50357.609333.7309-9.72819.40550.27682.1379-0.707-1.54980.30220.68311.3766-1.5593-0.57910.2759-0.1421-0.05870.9389-0.05510.3445.196814.94272.0058
108.44712.16995.02494.37871.86186.05540.02570.1903-0.1208-0.12730.0779-0.09580.02990.2891-0.10370.08820.02240.01780.14950.0380.148664.62667.426122.3964
1148.5988-10.961421.35223.12655.422622.56760.3382.3709-1.6631-2.1714-0.38062.2597-0.82250.270.04260.2648-0.0036-0.17410.2380.01440.351653.70793.035211.5055
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 17
2X-RAY DIFFRACTION2A18 - 24
3X-RAY DIFFRACTION3A25 - 42
4X-RAY DIFFRACTION4A43 - 51
5X-RAY DIFFRACTION5A52 - 64
6X-RAY DIFFRACTION6A65 - 70
7X-RAY DIFFRACTION7A71 - 77
8X-RAY DIFFRACTION8A78 - 87
9X-RAY DIFFRACTION9A88 - 94
10X-RAY DIFFRACTION10A95 - 113
11X-RAY DIFFRACTION11A114 - 120

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