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- PDB-1oot: Crystal structure of the SH3 domain from a S. cerevisiae hypothet... -

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Basic information

Entry
Database: PDB / ID: 1oot
TitleCrystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution
ComponentsHypothetical 40.4 kDa protein in PES4-HIS2 intergenic region
KeywordsSTRUCTURAL GENOMICS / SH3 DOMAIN / STURCTURAL GENOMICS
Function / homology
Function and homology information


actin cortical patch localization / actin cortical patch / cellular bud neck / actin filament bundle assembly / phosphatidylinositol binding / actin filament binding / mitochondrion / identical protein binding / cytoplasm
Similarity search - Function
: / SH3YL1-like, SYLF domain / Ysc84 actin-binding domain / Las17-binding protein actin regulator / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...: / SH3YL1-like, SYLF domain / Ysc84 actin-binding domain / Las17-binding protein actin regulator / SH3 Domains / SH3 domain / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
LAS seventeen-binding protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsKursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: Crystal structure of the SH3 domain from a S. cerevisiae hypothetical 40.4 kDa protein at 1.39 A resolution
Authors: Kursula, P. / Lehmann, F. / Song, Y.H. / Wilmanns, M.
History
DepositionMar 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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: Hypothetical 40.4 kDa protein in PES4-HIS2 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6884
Polymers6,5811
Non-polymers1063
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.930, 39.930, 69.490
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hypothetical 40.4 kDa protein in PES4-HIS2 intergenic region


Mass: 6581.299 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: YFR024C / Production host: Escherichia coli (E. coli) / References: UniProt: P43603
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 1.98 Å3/Da / Density % sol: 37.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5 / Details: 70% MPD, pH 7.5, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8028 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8028 Å / Relative weight: 1
ReflectionResolution: 1.38→30 Å / Num. all: 13185 / Num. obs: 13185 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 21.65 Å2 / Rsym value: 0.056 / Net I/σ(I): 15
Reflection shellResolution: 1.38→1.44 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 1398 / Rsym value: 0.414 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SEM

1sem


Resolution: 1.39→20 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.018 / SU ML: 0.038
Isotropic thermal model: ISOTROPIC, AT LATE STAGES OF REFINEMENT ANISOTROPIC
Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / Stereochemistry target values: Engh & Huber
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS DURING REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.17046 656 5 %RANDOM
Rwork0.13207 ---
all0.13397 13120 --
obs0.13397 13120 97.76 %-
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: 15.044 Å2
Baniso -1Baniso -2Baniso -3
1-1.17 Å20.58 Å20 Å2
2--1.17 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms515 0 3 60 578
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021536
X-RAY DIFFRACTIONr_bond_other_d0.0030.02474
X-RAY DIFFRACTIONr_angle_refined_deg1.8421.936739
X-RAY DIFFRACTIONr_angle_other_deg0.87931112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.179571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.276
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02635
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02117
X-RAY DIFFRACTIONr_nbd_refined0.190.279
X-RAY DIFFRACTIONr_nbd_other0.2460.2576
X-RAY DIFFRACTIONr_nbtor_other0.090.2336
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.226
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3660.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2580.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it2.9914330
X-RAY DIFFRACTIONr_mcangle_it4.0755542
X-RAY DIFFRACTIONr_scbond_it3.9924206
X-RAY DIFFRACTIONr_scangle_it5.9185197
X-RAY DIFFRACTIONr_rigid_bond_restr2.2462536
X-RAY DIFFRACTIONr_sphericity_free7.14263
X-RAY DIFFRACTIONr_sphericity_bonded5.1262515
LS refinement shellResolution: 1.39→1.426 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 45 -
Rwork0.264 841 -
obs-841 92 %

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