[English] 日本語
Yorodumi
- PDB-3ps8: Crystal structure of L68V mutant of human cystatin C -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more