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- PDB-2a08: Structure of the yeast YHH6 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 2a08
TitleStructure of the yeast YHH6 SH3 domain
ComponentsHypothetical 41.8 kDa protein in SPO13-ARG4 intergenic region
KeywordsPROTEIN BINDING / sh3 domain / yeast / structural genomics
Function / homology
Function and homology information


actin cortical patch localization / actin cortical patch / actin filament bundle assembly / phosphatidylinositol binding / endocytosis / actin filament binding / actin cytoskeleton organization / cytosol
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
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKursula, P. / Kursula, I. / Song, Y.H. / Lehmann, F. / Zou, P. / Wilmanns, M.
CitationJournal: To be Published
Title: 3-D proteome of yeast SH3 domains
Authors: Kursula, P. / Kursula, I. / Song, Y.H. / Lehmann, F. / Zou, P. / Wilmanns, M.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 23, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical 41.8 kDa protein in SPO13-ARG4 intergenic region
B: Hypothetical 41.8 kDa protein in SPO13-ARG4 intergenic region


Theoretical massNumber of molelcules
Total (without water)13,0272
Polymers13,0272
Non-polymers00
Water4,125229
1
A: Hypothetical 41.8 kDa protein in SPO13-ARG4 intergenic region


Theoretical massNumber of molelcules
Total (without water)6,5131
Polymers6,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical 41.8 kDa protein in SPO13-ARG4 intergenic region


Theoretical massNumber of molelcules
Total (without water)6,5131
Polymers6,5131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.830, 66.830, 52.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64
Components on special symmetry positions
IDModelComponents
11A-128-

HOH

21A-179-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 6 - 62 / Label seq-ID: 4 - 60

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Hypothetical 41.8 kDa protein in SPO13-ARG4 intergenic region


Mass: 6513.289 Da / Num. of mol.: 2 / Fragment: sh3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32793
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.4 M ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9537 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 24, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.54→40 Å / Num. obs: 19553 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Rsym value: 0.06 / Net I/σ(I): 15.5
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.6 / Rsym value: 0.307 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1OOT

1oot


Resolution: 1.54→33.41 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.503 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.077 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21547 977 5 %RANDOM
Rwork0.17109 ---
obs0.17329 18569 98.28 %-
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: 10.595 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.05 Å20 Å2
2--0.11 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.54→33.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms920 0 0 229 1149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022940
X-RAY DIFFRACTIONr_bond_other_d0.0020.02828
X-RAY DIFFRACTIONr_angle_refined_deg1.4541.9241270
X-RAY DIFFRACTIONr_angle_other_deg0.81131933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0275114
X-RAY DIFFRACTIONr_chiral_restr0.0950.2135
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021054
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02200
X-RAY DIFFRACTIONr_nbd_refined0.20.2162
X-RAY DIFFRACTIONr_nbd_other0.2540.2998
X-RAY DIFFRACTIONr_nbtor_other0.0830.2565
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.2119
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3330.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.221
X-RAY DIFFRACTIONr_mcbond_it1.2483575
X-RAY DIFFRACTIONr_mcangle_it1.8654919
X-RAY DIFFRACTIONr_scbond_it2.1984365
X-RAY DIFFRACTIONr_scangle_it3.2225351
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
333medium positional0.290.5
457loose positional0.715
333medium thermal1.042
457loose thermal1.7110
LS refinement shellResolution: 1.541→1.581 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.249 69
Rwork0.197 1302

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