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- PDB-3ul6: Saccharum officinarum canecystatin-1 in space group P6422 -

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Basic information

Entry
Database: PDB / ID: 3ul6
TitleSaccharum officinarum canecystatin-1 in space group P6422
ComponentsCanecystatin-1
KeywordsHYDROLASE INHIBITOR / Cystatin / Defense
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / identical protein binding
Similarity search - Function
Aspartic acid proteinase inhibitor / Cystatin / 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
Cysteine proteinase inhibitor
Similarity search - Component
Biological speciesSaccharum officinarum (noble cane)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.63 Å
AuthorsValadares, N.F. / Pereira, H.M. / Oliveira-Silva, R. / Garratt, R.C.
CitationJournal: Febs J. / Year: 2013
Title: X-ray crystallography and NMR studies of domain-swapped canecystatin-1.
Authors: Valadares, N.F. / de Oliveira-Silva, R. / Cavini, I.A. / Marques, I.A. / Pereira, H.D. / Soares-Costa, A. / Henrique-Silva, F. / Kalbitzer, H.R. / Munte, C.E. / Garratt, R.C.
History
DepositionNov 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Canecystatin-1
B: Canecystatin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0893
Polymers30,7352
Non-polymers3541
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4370 Å2
ΔGint-28 kcal/mol
Surface area9650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.800, 83.800, 142.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein Canecystatin-1


Mass: 15367.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharum officinarum (noble cane) / Gene: cystatin-1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7Y0Q9
#2: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.38 Å3/Da / Density % sol: 48.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.75
Details: 100mM HEPES, 200mM MgCl2, 25% PEG4000, pH 7.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.45 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 26, 2008 / Details: Si(111)
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.45 Å / Relative weight: 1
ReflectionResolution: 2.63→50.1 Å / Num. all: 9392 / Num. obs: 9139 / % possible obs: 97.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellHighest resolution: 2.63 Å / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX2011_09_22_2056refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.63→50.855 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.69 / σ(F): 1.36 / Phase error: 22.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2503 436 4.78 %
Rwork0.2386 --
obs0.2391 9125 97.6 %
all-9392 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 70.453 Å2 / ksol: 0.36 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7314 Å2-0 Å2-0 Å2
2--3.7314 Å2-0 Å2
3----7.4629 Å2
Refinement stepCycle: LAST / Resolution: 2.63→50.855 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1218 0 18 21 1257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091263
X-RAY DIFFRACTIONf_angle_d1.1151704
X-RAY DIFFRACTIONf_dihedral_angle_d18.203435
X-RAY DIFFRACTIONf_chiral_restr0.073187
X-RAY DIFFRACTIONf_plane_restr0.003217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.63-3.01060.31671640.3192767X-RAY DIFFRACTION97
3.0106-3.79280.25441390.22642880X-RAY DIFFRACTION99
3.7928-50.86480.22821330.2273042X-RAY DIFFRACTION97
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)
11.41540.00030.93891.51780.12151.5343-0.03210.0428-0.36090.07190.0197-0.24510.05250.1110.02380.2225-0.0010.0010.44790.00070.42177.13932.64334.2772
21.6610.19440.41121.45470.03141.6518-0.04760.0117-0.2641-0.08850.0527-0.0881-0.08910.1134-0.02720.2708-0.0375-0.01370.4352-0.00540.33066.509334.53924.9332
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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