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- PDB-6lsq: Crystal structure of Echistatin, an RGD-containing short disintegrin -

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Basic information

Entry
Database: PDB / ID: 6lsq
TitleCrystal structure of Echistatin, an RGD-containing short disintegrin
ComponentsDisintegrin
KeywordsBLOOD CLOTTING / Disintegrin / Platelet aggregation inhibitor
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Disintegrin, conserved site / Disintegrins signature. / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin ...Disintegrin, conserved site / Disintegrins signature. / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature.
Similarity search - Domain/homology
Disintegrin metalloproteinase/disintegrin echistatin
Similarity search - Component
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsChang, Y.T. / Chen, Y.C. / Chuang, W.J.
Funding support1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan)
CitationJournal: Toxins / Year: 2020
Title: Structural Insight into Integrin Recognition and Anticancer Activity of Echistatin.
Authors: Chen, Y.C. / Chang, Y.T. / Chen, C.Y. / Shiu, J.H. / Cheng, C.H. / Huang, C.H. / Chen, J.F. / Chuang, W.J.
History
DepositionJan 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disintegrin
B: Disintegrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5193
Polymers11,4232
Non-polymers961
Water59433
1
A: Disintegrin


Theoretical massNumber of molelcules
Total (without water)5,7111
Polymers5,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area4110 Å2
MethodPISA
2
B: Disintegrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,8082
Polymers5,7111
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.906, 33.906, 121.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Disintegrin / Echistatin


Mass: 5711.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Echis carinatus (saw-scaled viper) / Production host: Komagataella pastoris (fungus) / References: UniProt: E9JGG9
#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.: 33 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.8 Å3/Da / Density % sol: 31.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M Bicine pH9.0 2.55M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 0.99984 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 7695 / % possible obs: 92.5 % / Redundancy: 4.9 % / CC1/2: 0.991 / Net I/σ(I): 7.88
Reflection shellResolution: 1.8→1.91 Å / Mean I/σ(I) obs: 2.96 / Num. unique obs: 2099 / CC1/2: 0.951

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDS20190315data reduction
XDS20190315data scaling
XDS20190315phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RQG

4rqg


Resolution: 1.8→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.925 / SU B: 7.493 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.255 419 5.3 %RANDOM
Rwork0.212 ---
obs0.21226 7541 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.851 Å2
Baniso -1Baniso -2Baniso -3
1-0.93 Å20.47 Å20 Å2
2--0.93 Å2-0 Å2
3----3.03 Å2
Refinement stepCycle: 1 / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 5 33 796
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013783
X-RAY DIFFRACTIONr_bond_other_d0.0010.018669
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.6881050
X-RAY DIFFRACTIONr_angle_other_deg1.3331.6161580
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.889596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67921.66748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55515141
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.857158
X-RAY DIFFRACTIONr_chiral_restr0.0870.296
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.02887
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02161
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7892.179390
X-RAY DIFFRACTIONr_mcbond_other1.7872.179389
X-RAY DIFFRACTIONr_mcangle_it2.6463.246484
X-RAY DIFFRACTIONr_mcangle_other2.6443.247485
X-RAY DIFFRACTIONr_scbond_it2.612.694391
X-RAY DIFFRACTIONr_scbond_other2.6082.686387
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2653.873560
X-RAY DIFFRACTIONr_long_range_B_refined5.40425.904800
X-RAY DIFFRACTIONr_long_range_B_other5.425.859798
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 21 -
Rwork0.261 538 -
obs--95.88 %
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)
10.8743-0.28751.66940.4437-0.1643.67030.0164-0.1958-0.07040.01460.13060.0177-0.0043-0.3629-0.14710.05220.030.00160.14540.03650.0114-19.66547.493619.1712
20.7388-0.22280.45680.1677-0.44121.26170.0074-0.0175-0.0585-0.00410.0093-0.0032-0.0254-0.0042-0.01660.0457-0.01630.00410.0268-0.0060.0541-13.37556.9433.3376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 45
2X-RAY DIFFRACTION2B-1 - 49

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