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- PDB-1j2l: Crystal structure of the disintegrin, trimestatin -

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Basic information

Entry
Database: PDB / ID: 1j2l
TitleCrystal structure of the disintegrin, trimestatin
ComponentsDisintegrin triflavin
KeywordsTOXIN / disintegrin / RGD motif / trimestatin / snake venom
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Disintegrin triflavin
Similarity search - Component
Biological speciesTrimeresurus flavoviridis (habu)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsFujii, Y. / Okuda, D. / Fujimoto, Z. / Morita, T. / Mizuno, H.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of Trimestatin, a Disintegrin Containing a Cell Adhesion Recognition Motif RGD
Authors: Fujii, Y. / Okuda, D. / Fujimoto, Z. / Horii, T. / Morita, T. / Mizuno, H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary crystallographic studies of dimeric disintegrins from the venom of two Agkistrodon snakes.
Authors: Fujii, Y. / Okuda, D. / Fujimoto, Z. / Morita, T. / Mizuno, H.
#2: Journal: J.Biochem.(Tokyo) / Year: 2001
Title: Purification and characterization of a new RGD/KGD-containing dimeric disintegrin, piscivostatin, from the venom of Agkistrodon piscivorus piscivorus: the unique effect of piscivostatin on platelet aggregation.
Authors: Okuda, D. / Morita, T.
History
DepositionJan 6, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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
A: Disintegrin triflavin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6832
Polymers7,5871
Non-polymers961
Water2,756153
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.546, 48.119, 37.667
Angle α, β, γ (deg.)90.00, 126.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Disintegrin triflavin / trimestatin / RGD-containing peptide


Mass: 7586.620 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Trimeresurus flavoviridis (habu) / Secretion: venom / References: UniProt: P21859
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 1.86 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG 8000, ammonium sulfate, pH 7.0, VAPOR DIFFUSION, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130.0 mg/mlprotein11
230 %(w/v)PEG800012
30.1 Mammonium sulfate12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 11, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 7539 / Num. obs: 52379 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.056 / Net I/σ(I): 8.4
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1092 / Rsym value: 0.242 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 30 Å / Num. obs: 7539 / Num. measured all: 52379 / Rmerge(I) obs: 0.056
Reflection shell
*PLUS
Lowest resolution: 1.76 Å / Num. unique obs: 1092 / Num. measured obs: 7548 / Rmerge(I) obs: 0.242

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVL

1fvl


Resolution: 1.7→18.31 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 1415224.78 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 387 5.1 %RANDOM
Rwork0.187 ---
obs0.187 52379 99.7 %-
all-7538 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.1676 Å2 / ksol: 0.33892 e/Å3
Displacement parametersBiso mean: 23.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å21 Å2
2---0.09 Å20 Å2
3---0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.04 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 1.7→18.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms506 0 5 153 664
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it2.122
X-RAY DIFFRACTIONc_scbond_it2.172
X-RAY DIFFRACTIONc_scangle_it3.292.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.233 66 5.3 %
Rwork0.224 1170 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CIS_PEPTIDE.PARAM
Refinement
*PLUS
Lowest resolution: 30 Å / Num. reflection all: 52379 / Num. reflection obs: 7538 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / Rfactor Rwork: 0.229 / Num. reflection Rwork: 737

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