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- PDB-1xod: Crystal structure of X. tropicalis Spred1 EVH-1 domain -

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Basic information

Entry
Database: PDB / ID: 1xod
TitleCrystal structure of X. tropicalis Spred1 EVH-1 domain
ComponentsSpred1
KeywordsSIGNALING PROTEIN / Spred / Sprouty / EVH1 / Peptide-binding
Function / homology
Function and homology information


FGFRL1 modulation of FGFR1 signaling / negative regulation of MAPK cascade / phosphatase binding / protein kinase binding / plasma membrane
Similarity search - Function
c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 ...c-Kit-binding domain / SPRE, EVH1 domain / KBD domain profile. / Sprouty / Sprouty protein (Spry) / Sprouty (SPR) domain profile. / WH1/EVH1 domain / WH1 domain / WH1 domain profile. / WASP homology region 1 / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Sprouty-related, EVH1 domain-containing protein 1
Similarity search - Component
Biological speciesXenopus tropicalis (tropical clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsHarmer, N.J. / Sivak, J.M. / Amaya, E. / Blundell, T.L.
CitationJournal: Febs Lett. / Year: 2005
Title: 1.15A Crystal structure of the X. tropicalis Spred1 EVH1 domain suggests a fourth distinct peptide-binding mechanism within the EVH1 family
Authors: Harmer, N.J. / Sivak, J.M. / Amaya, E. / Blundell, T.L.
History
DepositionOct 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 23, 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_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

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Assembly

Deposited unit
A: Spred1
B: Spred1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0333
Polymers25,9412
Non-polymers921
Water6,575365
1
A: Spred1


Theoretical massNumber of molelcules
Total (without water)12,9711
Polymers12,9711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Spred1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0632
Polymers12,9711
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.811, 38.193, 79.907
Angle α, β, γ (deg.)90.00, 95.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Spred1


Mass: 12970.538 Da / Num. of mol.: 2 / Fragment: EVH-1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus tropicalis (tropical clawed frog)
Gene: Spred1 / Plasmid: pETG-10a / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: Q66JG9
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / 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: 1.92 Å3/Da / Density % sol: 35.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 3350, potassium fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 22, 2004 / Details: mirrors
RadiationMonochromator: RH COATED SILICA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.15→79 Å / Num. all: 68977 / Num. obs: 68977 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 7.84 Å2 / Rsym value: 0.069 / Net I/σ(I): 19.4
Reflection shellResolution: 1.15→1.17 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.99 / Num. unique all: 3330 / Rsym value: 0.351 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entries 1EVH, 1I7A, 1QC6

1evh

1i7a

1qc6


Resolution: 1.15→79.06 Å / Cor.coef. Fo:Fc: 0.97 / SU B: 0.389 / SU ML: 0.019 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.177 3471 -random
Rwork0.154 ---
all0.155 68977 --
obs0.15538 68977 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 9.283 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20 Å2-0.17 Å2
2--0.06 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.15→79.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1694 0 6 365 2065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211798
X-RAY DIFFRACTIONr_bond_other_d0.0030.021687
X-RAY DIFFRACTIONr_angle_refined_deg1.3351.9412430
X-RAY DIFFRACTIONr_angle_other_deg0.83333871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475220
X-RAY DIFFRACTIONr_chiral_restr0.0790.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021997
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02413
X-RAY DIFFRACTIONr_nbd_refined0.2010.2340
X-RAY DIFFRACTIONr_nbd_other0.260.22065
X-RAY DIFFRACTIONr_nbtor_other0.0850.21168
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4870.234
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3240.2141
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.273
X-RAY DIFFRACTIONr_mcbond_it0.941.51110
X-RAY DIFFRACTIONr_mcangle_it1.53621796
X-RAY DIFFRACTIONr_scbond_it1.7523688
X-RAY DIFFRACTIONr_scangle_it2.684.5634
X-RAY DIFFRACTIONr_rigid_bond_restr0.94721798
X-RAY DIFFRACTIONr_sphericity_free2.2172365
X-RAY DIFFRACTIONr_sphericity_bonded1.85521769
LS refinement shellResolution: 1.15→1.177 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 261 -
Rwork0.167 4829 -
obs-4568 94.5 %

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