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- PDB-2w9p: Crystal Structure of Potato Multicystatin -

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Basic information

Entry
Database: PDB / ID: 2w9p
TitleCrystal Structure of Potato Multicystatin
ComponentsMULTICYSTATIN
KeywordsHYDROLASE INHIBITOR / PROTEASE INHIBITOR / THIOL PROTEASE INHIBITOR
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity
Similarity search - Function
Cystatin / 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 speciesSOLANUM TUBEROSUM (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.7 Å
AuthorsNissen, M.S. / Kumar, G.N. / Youn, B. / Knowles, D.B. / Lam, K.S. / Ballinger, W.J. / Knowles, N.R. / Kang, C.
CitationJournal: Plant Cell / Year: 2009
Title: Characterization of Solanum Tuberosum Multicystatin and its Structural Comparison with Other Cystatins.
Authors: Nissen, M.S. / Kumar, G.N. / Youn, B. / Knowles, D.B. / Lam, K.S. / Ballinger, W.J. / Knowles, N.R. / Kang, C.
History
DepositionJan 28, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MULTICYSTATIN
B: MULTICYSTATIN
C: MULTICYSTATIN
D: MULTICYSTATIN
E: MULTICYSTATIN
F: MULTICYSTATIN
G: MULTICYSTATIN
H: MULTICYSTATIN
I: MULTICYSTATIN
J: MULTICYSTATIN
K: MULTICYSTATIN
L: MULTICYSTATIN
M: MULTICYSTATIN
N: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)142,06814
Polymers142,06814
Non-polymers00
Water0
1
A: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
13
M: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
14
N: MULTICYSTATIN


Theoretical massNumber of molelcules
Total (without water)10,1481
Polymers10,1481
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)210.850, 85.710, 96.860
Angle α, β, γ (deg.)90.00, 100.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
MULTICYSTATIN / MC / POTATO MULTICYSTATIN


Mass: 10147.722 Da / Num. of mol.: 14 / Fragment: RESIDUES 100-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SOLANUM TUBEROSUM (potato) / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ER2566 / References: UniProt: P37842

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.06 Å3/Da / Density % sol: 59.5 % / Description: NONE

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0332
DetectorType: ADSC IMAGE PLATE / Detector: IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 40548 / % possible obs: 88.4 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.06

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Processing

SoftwareName: X-PLOR / Version: NULL / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→10 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.246 --
Rwork0.212 --
obs0.212 34671 75.6 %
Refinement stepCycle: LAST / Resolution: 2.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10038 0 0 0 10038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.19
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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