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- PDB-1cew: THE 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF CHICKEN EGG WHITE CY... -

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Basic information

Entry
Database: PDB / ID: 1cew
TitleTHE 2.0 ANGSTROMS X-RAY CRYSTAL STRUCTURE OF CHICKEN EGG WHITE CYSTATIN AND ITS POSSIBLE MODE OF INTERACTION WITH CYSTEINE PROTEINASES
ComponentsCYSTATIN
KeywordsPROTEINASE INHIBITOR(CYSTEINE)
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / vesicle / extracellular space / 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 speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsBode, W. / Musil, D. / Huber, R.
Citation
Journal: EMBO J. / Year: 1988
Title: The 2.0 A X-ray crystal structure of chicken egg white cystatin and its possible mode of interaction with cysteine proteinases.
Authors: Bode, W. / Engh, R. / Musil, D. / Thiele, U. / Huber, R. / Karshikov, A. / Brzin, J. / Kos, J. / Turk, V.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Conformational Variability of Chicken Cystatin: Comparison of Structures Determined by X-Ray Diffraction and NMR-Spectroscopy
Authors: Engh, R.A. / Dieckmann, T. / Bode, W. / Auerswald, E.A. / Turk, V. / Huber, R. / Oschkinat, H.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: The Structures of Native Phosphorylated Chicken Cystatin and of a Recombinant Unphosphorylated Variant in Solution
Authors: Dieckmann, T. / Mitschang, L. / Hofmann, M. / Kos, J. / Turk, V. / Auerswald, E.A. / Jaenicke, R. / Oschkinat, H.
#3: Journal: FEBS Lett. / Year: 1991
Title: The Cystatins: Protein Inhibitors of Cysteine Proteinases
Authors: Turk, V. / Bode, W.
#4: Journal: Biol.Chem.Hoppe-Seyler / Year: 1990
Title: Mechanism of Interaction of Cysteine Proteinases and Their Protein Inhibitors as Compared to the Serine Proteinase-Inhibitor Interaction
Authors: Bode, W. / Engh, R. / Musil, D. / Laber, B. / Stubbs, M. / Huber, R. / Turk, V.
#5: Journal: FEBS Lett. / Year: 1989
Title: Mechanism of Inhibition of Papain by Chicken Egg White Cystatin: Inhibition Constants of N-Terminally Truncated Forms and Cyanogen Bromide Fragments of the Inhibitor
Authors: Machleidt, W. / Thiele, U. / Laber, B. / Assfalg-Machleidt, I. / Esterl, A. / Wiegand, G. / Kos, J. / Turk, V. / Bode, W.
#6: Journal: FEBS Lett. / Year: 1989
Title: The Cysteine Proteinase Inhibitor Chicken Cystatin is a Phophoprotein
Authors: Laber, B. / Krieglstein, K. / Henschen, A. / Kos, J. / Turk, V. / Huber, R. / Bode, W.
History
DepositionApr 21, 1993Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Sep 7, 2011Group: Other
Revision 1.4Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: CYSTATIN


Theoretical massNumber of molelcules
Total (without water)12,2051
Polymers12,2051
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.900, 47.900, 87.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Atom site foot note1: GLU I 88 - MET I 89 OMEGA =121.89 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

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Components

#1: Protein CYSTATIN


Mass: 12204.868 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Organ: EGG / References: UniProt: P01038
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal grow
*PLUS
pH: 8.2 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl11
211NaCl

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 6715 / % possible obs: 75 % / Rmerge(I) obs: 0.105
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.2 Å / % possible obs: 30 %

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Processing

SoftwareName: EREF / Classification: refinement
RefinementRfactor Rwork: 0.198 / Highest resolution: 2 Å
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms854 0 0 123 977
Software
*PLUS
Name: EREF / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 6 Å / Num. reflection obs: 6181 / Rfactor obs: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.017
X-RAY DIFFRACTIONo_angle_deg3.5

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