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

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Basic information

Entry
Database: PDB / ID: 3qrd
TitleCrystal structure of L68V mutant of human cystatin C
ComponentsCystatin-C
KeywordsHYDROLASE INHIBITOR / cysteine protease inhibitor / 3D domain swapping / protein / 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 / 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
DI(HYDROXYETHYL)ETHER / Cystatin-C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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. / Borek, D. / Otwinowski, Z. / Skowron, P. / Szymanska, A.
History
DepositionFeb 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 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 / 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

Downloads & links

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Assembly

Deposited unit
A: Cystatin-C
B: Cystatin-C
C: Cystatin-C
D: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,04110
Polymers53,4044
Non-polymers6376
Water1,946108
1
A: Cystatin-C
B: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9144
Polymers26,7022
Non-polymers2122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-33 kcal/mol
Surface area13330 Å2
MethodPISA
2
C: Cystatin-C
D: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1276
Polymers26,7022
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6560 Å2
ΔGint-38 kcal/mol
Surface area13180 Å2
MethodPISA
3
A: Cystatin-C
B: Cystatin-C
hetero molecules

A: Cystatin-C
B: Cystatin-C
hetero molecules

C: Cystatin-C
D: Cystatin-C
hetero molecules

C: Cystatin-C
D: Cystatin-C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,08220
Polymers106,8098
Non-polymers1,27312
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
crystal symmetry operation1_454x-1,y,z-11
crystal symmetry operation2_655-x+1,y,-z1
Buried area32430 Å2
ΔGint-180 kcal/mol
Surface area48110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.123, 89.876, 65.154
Angle α, β, γ (deg.)90.00, 107.03, 90.00
Int Tables number5
Space group name H-MC121

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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.: 4 / 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(de3) / References: UniProt: P01034
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.18M tri-Sodium citrate, 0.1M TrisHCl pH 8.0, 30% PEG, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 21, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.14→50 Å / Num. obs: 28962 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 33.889
Reflection shellResolution: 2.14→2.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 2.09 / % possible all: 99.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
MOLREPphasing
REFMAC5.5.0110refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G96
Resolution: 2.19→36.45 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.846 / SU B: 17.444 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29325 1204 5 %RANDOM
Rwork0.2137 ---
obs0.21766 23060 83.06 %-
all-28962 --
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: 16.196 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å2-1.49 Å2
2--1.32 Å20 Å2
3----1.06 Å2
Refinement stepCycle: LAST / Resolution: 2.19→36.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3409 0 42 108 3559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223559
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9414801
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5585437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.95723.736174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.15815593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.731529
X-RAY DIFFRACTIONr_chiral_restr0.0850.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212715
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_it4.1091.52181
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.53623517
X-RAY DIFFRACTIONr_scbond_it9.63531378
X-RAY DIFFRACTIONr_scangle_it12.0624.51283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.19→2.249 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 26 -
Rwork0.22 516 -
obs--25.53 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
114.41730.1664.67410.2591-1.503917.83690.46820.0185-0.25810.0314-0.4596-1.32810.87391.1293-0.00860.24050.08160.08710.10810.05480.310335.383832.0439-41.7721
248.385311.4241-6.770825.34541.584229.2048-0.21931.7046-0.4422-1.29990.2641-0.11570.4773-0.6777-0.04490.23820.04650.08180.1252-0.02050.082325.71329.0952-48.3381
314.318-4.3016-8.895710.5109-0.76156.89510.2165-0.65770.27680.0190.27820.8839-0.14970.0855-0.49470.1883-0.078-0.02871.0489-0.21270.278513.158432.0802-38.3875
45.1375-1.46432.42965.3705-1.34673.7278-0.1933-0.43960.57140.3506-0.11730.2793-0.1881-0.56160.31060.1979-0.02420.06180.1422-0.05790.189722.596835.3031-40.856
53.30060.09541.78513.31381.01654.59480.0935-0.2448-0.00690.3394-0.18-0.29380.03510.24510.08640.1265-0.03760.07890.08190.04040.196742.78045.2169-14.0927
621.95885.5024-8.88555.3462-4.123317.32710.1714-1.257-1.48050.9705-0.163-0.38681.31110.137-0.00830.6001-0.05240.0130.15280.12870.309444.085-4.0664-2.6464
74.5732-0.78322.81543.93150.94328.0964-0.1999-0.22950.2110.4873-0.0550.2203-0.784-0.56710.25480.18510.04950.0430.0472-0.05280.20235.13419.2796-19.9485
819.85024.30421.94097.27190.913614.57710.0966-1.5328-0.52720.7844-0.1643-0.36150.3572-0.49980.06770.2284-0.01390.10460.1437-0.00810.20432.3494-43.0476-30.8437
96.07110.60225.544916.5388-10.508328.6776-0.0508-0.16360.45770.1896-0.01030.5966-0.311-0.60090.0610.09710.05310.06080.0954-0.08380.279428.3721-37.0445-41.3649
103.4038-0.36941.24995.729-0.31585.370.12080.42940.154-0.4109-0.1781-0.09090.20210.30010.05730.07690.01150.09970.0852-0.03210.218632.4984-39.902-46.4509
116.8113-0.56022.73173.64361.16425.04790.37751.0790.64910.0648-0.5033-0.1782-0.24980.53160.12580.13520.07180.07060.35430.080.138352.6758-10.0298-21.5942
1227.286-12.9988-2.262613.31481.066326.0832-0.5729-0.19540.23261.96390.3586-0.06170.67620.73660.21430.45230.00510.01450.3042-0.01580.151162.7029-9.9245-10.8546
137.16930.48122.30725.85270.77617.6833-0.140.84220.54-0.31690.0267-0.1302-0.61030.65260.11330.18060.07720.05640.28610.04940.180551.639-9.8819-22.4144
148.97654.6794-2.158432.2514-12.637811.87250.49011.29530.2176-0.6401-0.26390.36580.2410.5616-0.22620.12350.16650.04880.4636-0.06950.152350.4136-14.2996-27.9121
1576.53152.957120.6657.2066-2.446812.00311.63331.45-1.1854-0.5286-0.69990.06841.99260.5019-0.93340.9740.0619-0.14970.4307-0.18450.621888.59884.9982-2.0351
167.928132.32150.3198203.91932.95340.0557-4.56292.7929-1.5836-0.41144.81033.51790.25050.0208-0.24746.3915-2.49312.81032.7681-1.26222.847394.782411.5512-0.9114
175.1609-3.9827-0.03428.755213.07730.40390.0316-0.27010.124-0.43030.2226-0.2856-1.0129-0.1084-0.25420.3121-0.1547-0.00840.27890.06590.287287.687521.73236.3385
183.4093-0.36442.48063.28841.08528.26950.1344-0.1525-0.26250.22380.03710.10970.8699-0.4119-0.17150.185-0.11220.06970.23080.07780.20386.505915.562410.0482
197.02721.54561.20631.17110.06371.6906-0.01960.04230.7827-0.06890.07640.2576-0.17850.1801-0.05680.2868-0.09860.06070.12120.01780.260460.200919.5052-14.7886
209.88831.41-2.424912.65192.474733.992-0.1315-0.42041.3197-0.44630.09760.6517-2.1275-0.36370.03390.409-0.1327-0.05720.17680.08910.610147.542223.8669-17.3562
2116.6148-4.4654-3.59855.41471.38735.42160.12190.09670.01350.0442-0.20320.45280.0324-0.27610.08130.37-0.25960.00690.19950.00790.307863.416620.7667-12.0927
2238.046-28.3603-14.028323.728811.77211.4889-0.9359-1.53191.4970.38211.1387-0.6916-0.23310.8491-0.20280.4694-0.1518-0.06880.3489-0.13740.514762.682726.6575-4.4981
2357.6997-39.088233.150726.5828-22.323619.407-1.0876-0.77440.81360.87760.6705-0.5567-0.7042-0.15140.41710.60030.02010.02720.4031-0.06560.360780.992-15.06221.3034
2420.6385-4.6537-13.7495.47535.349710.9138-0.1719-0.4583-0.26650.55750.0548-0.09920.48260.44920.1170.29480.1279-0.03390.11930.0360.249393.0449-27.090514.6834
252.4591-0.25671.54290.0636-0.22121.22390.06990.04980.154-0.012-0.035-0.0203-0.0671-0.0021-0.03480.26550.08330.1070.10820.00680.263581.1027-24.26975.4325
2610.4399-3.5702-6.2736.45121.44673.8685-0.19560.1475-0.2009-0.28720.0830.05060.1737-0.06230.11260.16610.06710.00010.3418-0.05590.084261.9394-24.7561-20.9874
271.3574-0.3258-1.49291.67610.820310.64590.04150.05920.16670.01710.1323-0.1620.33130.3361-0.17380.16630.08050.07480.2006-0.03130.181971.7506-26.6462-3.8647
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 19
2X-RAY DIFFRACTION2A20 - 25
3X-RAY DIFFRACTION3A26 - 40
4X-RAY DIFFRACTION4A41 - 58
5X-RAY DIFFRACTION5A59 - 81
6X-RAY DIFFRACTION6A82 - 92
7X-RAY DIFFRACTION7A93 - 120
8X-RAY DIFFRACTION8B12 - 22
9X-RAY DIFFRACTION9B23 - 33
10X-RAY DIFFRACTION10B34 - 57
11X-RAY DIFFRACTION11B58 - 76
12X-RAY DIFFRACTION12B77 - 82
13X-RAY DIFFRACTION13B83 - 106
14X-RAY DIFFRACTION14B107 - 120
15X-RAY DIFFRACTION15C13 - 19
16X-RAY DIFFRACTION16C20 - 24
17X-RAY DIFFRACTION17C25 - 38
18X-RAY DIFFRACTION18C39 - 55
19X-RAY DIFFRACTION19C56 - 80
20X-RAY DIFFRACTION20C81 - 87
21X-RAY DIFFRACTION21C88 - 113
22X-RAY DIFFRACTION22C114 - 120
23X-RAY DIFFRACTION23D10 - 20
24X-RAY DIFFRACTION24D21 - 40
25X-RAY DIFFRACTION25D41 - 73
26X-RAY DIFFRACTION26D74 - 91
27X-RAY DIFFRACTION27D92 - 120

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