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- PDB-1ukm: Crystal structure of EMS16, an Antagonist of collagen receptor in... -

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Basic information

Entry
Database: PDB / ID: 1ukm
TitleCrystal structure of EMS16, an Antagonist of collagen receptor integrin alpha2beta1 (GPIa/IIa)
Components
  • EMS16 A chain
  • EMS16 B chain
KeywordsTOXIN / Domain swapping / C-type lectin
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
: / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Snaclec EMS16 subunit beta / Snaclec EMS16 subunit alpha
Similarity search - Component
Biological speciesEchis multisquamatus (snake)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHorii, K. / Okuda, D. / Morita, T. / Mizuno, H.
Citation
Journal: Biochemistry / Year: 2003
Title: Structural characterization of EMS16, an Antagonist of collagen receptor (GPIa/IIa) from the venom of Echis multisquamatus
Authors: Horii, K. / Okuda, D. / Morita, T. / Mizuno, H.
#1: Journal: J.BIOCHEM.(TOKYO) / Year: 2003
Title: Characterization and Preliminary Crystallographic Studies of EMS16, an Antagonist of Collagen Receptor (GPIa/IIa) from the Venom of Echis multisquamatus
Authors: Okuda, D. / Horii, K. / Mizuno, H. / Morita, T.
#2: Journal: Biochemistry / Year: 2000
Title: Isolation and characterization of EMS16, a C-lectin type protein from Echis multisquamatus venom, a potent and selective inhibitor of the alpha2beta1 integrin
Authors: Marcinkiewicz, C. / Lobb, R.R. / Marcinkiewicz, M.M. / Daniel, J.L. / Smith, J.B. / Dangelmaier, C. / Weinreb, P.H. / Beacham, D.A. / Niewiarowski, S.
History
DepositionAug 27, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 25, 2018Group: Data collection / Database references / Structure summary
Category: pdbx_entry_details / struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Nov 20, 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

Downloads & links

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Assembly

Deposited unit
A: EMS16 A chain
B: EMS16 B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6368
Polymers31,0112
Non-polymers6256
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5110 Å2
ΔGint-21 kcal/mol
Surface area12930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.570, 59.933, 115.743
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein EMS16 A chain / EMS16 subunit A


Mass: 15889.537 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-134 / Source method: isolated from a natural source / Source: (natural) Echis multisquamatus (snake) / Secretion: venom / References: UniProt: Q7T2Q1
#2: Protein EMS16 B chain / EMS16 subunit B


Mass: 15121.384 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-128 / Mutation: G43S / Source method: isolated from a natural source / Source: (natural) Echis multisquamatus (snake) / Secretion: venom / References: UniProt: Q7T2Q0

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Sugars , 1 types, 1 molecules

#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 255 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsThe sequence database UNP Q7T2Q0 reports there is a conflict as Experimental Information.

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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: 2.39 Å3/Da / Density % sol: 48.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: PEG8000, potassium dihydrogen phosphate, glycerol, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
30.04 Mpotassium dihydrogen phosphate1reservoir
416 %PEG80001reservoir
520 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 12, 2002 / Details: Osmic confocal mirrors
RadiationMonochromator: Osmic confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→29.71 Å / Num. obs: 26199 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.031 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 5.6 / % possible all: 99.7
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 91401
Reflection shell
*PLUS
% possible obs: 99.7 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BJ3

1bj3


Resolution: 1.9→18.36 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1271064.4 / 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
Rfree0.233 1303 5 %RANDOM
Rwork0.196 ---
obs0.196 26143 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.6729 Å2 / ksol: 0.394865 e/Å3
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.12 Å20 Å20 Å2
2---1.31 Å20 Å2
3----2.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 39 250 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.21.5
X-RAY DIFFRACTIONc_mcangle_it3.842
X-RAY DIFFRACTIONc_scbond_it4.662
X-RAY DIFFRACTIONc_scangle_it6.272.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 209 4.9 %
Rwork0.274 4092 -
obs-4301 100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2HETERO.PARAMHETERO.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5CARBO_REP.PARAMCARBOHYDRATE.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.234
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81

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