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- PDB-1ggp: CRYSTAL STRUCTURE OF TRICHOSANTHES KIRILOWII LECTIN-1 AND ITS REL... -

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Basic information

Entry
Database: PDB / ID: 1ggp
TitleCRYSTAL STRUCTURE OF TRICHOSANTHES KIRILOWII LECTIN-1 AND ITS RELATION TO THE TYPE 2 RIBOSOME INACTIVATING PROTEINS
Components
  • PROTEIN (LECTIN 1 A CHAIN)
  • PROTEIN (LECTIN 1 B CHAIN)
KeywordsSUGAR BINDING PROTEIN / TRICHOSANTHES KIRILOWII / LECTIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
rRNA N-glycosylase / Sugar binding protein
Similarity search - Component
Biological speciesTrichosanthes kirilowii (Chinese cucumber)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsLi, M. / Chai, J.J. / Wang, Y.P. / Wang, K.Y. / Bi, R.C.
Citation
Journal: PROTEIN PEPT.LETT. / Year: 2003
Title: Crystal Structure of Trichosanthes Kirilowii Lectin-1 and its Relation to the Type 2 Ribosome Inactivating Proteins
Authors: Li, M. / Chai, J.J. / Wang, Y.P. / Wang, K.Y. / Bi, R.C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Molecular-Replacement Studies of Trichosanthes Kirilowii Lectin-1: a Structure Belonging to the Family of Type 2 Ribosome-inactivating Proteins.
Authors: Li, M. / Wang, Y.P. / Chai, J.J. / Wang, K.Y. / Bi, R.C.
History
DepositionSep 7, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (LECTIN 1 A CHAIN)
B: PROTEIN (LECTIN 1 B CHAIN)


Theoretical massNumber of molelcules
Total (without water)51,0302
Polymers51,0302
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-18 kcal/mol
Surface area20080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.960, 69.870, 180.960
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PROTEIN (LECTIN 1 A CHAIN) / TKL-1


Mass: 24383.979 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trichosanthes kirilowii (Chinese cucumber)
References: UniProt: Q7SIF0
#2: Protein PROTEIN (LECTIN 1 B CHAIN) / TKL-1


Mass: 26645.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Trichosanthes kirilowii (Chinese cucumber)
References: UniProt: Q7SIF1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growpH: 6
Details: Using the hanging-drop method, in which the droplets consisted of equal volume protein solution (4.2mg/ml) and the reservoir solution containing 15% PEG 8000, 0.5M Li2SO4 and 0.1M sodium ...Details: Using the hanging-drop method, in which the droplets consisted of equal volume protein solution (4.2mg/ml) and the reservoir solution containing 15% PEG 8000, 0.5M Li2SO4 and 0.1M sodium cacodylate buffer (pH 6.5). , pH 6.0

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 12480 / % possible obs: 74 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 0.088 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2.95 % / Mean I/σ(I) obs: 2 / Rsym value: 0.37 / % possible all: 68

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ABR

1abr


Resolution: 2.7→8 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.3 611 5.1 %RANDOM
Rwork0.225 ---
obs0.225 11928 76.2 %-
Displacement parametersBiso mean: 17.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 0 12 3587
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d29.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.63
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
LS refinement shellResolution: 2.7→2.86 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 74 5.6 %
Rwork0.273 1258 -
obs--52.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY

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