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- PDB-1zx6: High-resolution crystal structure of yeast Pin3 SH3 domain -

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Basic information

Entry
Database: PDB / ID: 1zx6
TitleHigh-resolution crystal structure of yeast Pin3 SH3 domain
ComponentsYpr154wp
KeywordsPROTEIN BINDING / SH3 domain
Function / homology
Function and homology information


Recycling pathway of L1 / RHOV GTPase cycle / negative regulation of Arp2/3 complex-mediated actin nucleation / actin cortical patch / Antigen processing: Ubiquitination & Proteasome degradation / Neutrophil degranulation / nucleus / cytoplasm
Similarity search - Function
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
[PSI+] inducibility protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKursula, P. / Kursula, I. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M.
CitationJournal: To be Published
Title: Structural genomics of yeast SH3 domains
Authors: Kursula, P. / Kursula, I. / Lehmann, F. / Zou, P. / Song, Y.H. / Wilmanns, M.
History
DepositionJun 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ypr154wp


Theoretical massNumber of molelcules
Total (without water)6,5161
Polymers6,5161
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.040, 27.360, 24.000
Angle α, β, γ (deg.)90.00, 102.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Ypr154wp


Mass: 6516.325 Da / Num. of mol.: 1 / Fragment: SH3 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pDEST-17 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06449
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.2 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. all: 7155 / Num. obs: 7155 / % possible obs: 94.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.069 / Net I/σ(I): 7.9
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 1187 / Rsym value: 0.312 / % possible all: 96.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 1oot

1oot


Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.335 / SU ML: 0.073 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS REFINEMENT / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.098 / ESU R Free: 0.1 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22089 358 5 %RANDOM
Rwork0.18157 ---
all0.18347 7155 --
obs0.18347 7155 94.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å20 Å20.36 Å2
2--2.73 Å20 Å2
3----1.75 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms448 0 0 59 507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.022461
X-RAY DIFFRACTIONr_bond_other_d0.0010.02396
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.99625
X-RAY DIFFRACTIONr_angle_other_deg0.783935
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.335555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.17725.65223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.2451574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.413151
X-RAY DIFFRACTIONr_chiral_restr0.0960.261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0290
X-RAY DIFFRACTIONr_nbd_refined0.1910.253
X-RAY DIFFRACTIONr_nbd_other0.1730.2373
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2211
X-RAY DIFFRACTIONr_nbtor_other0.0850.2233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.230
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3790.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1640.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.27
X-RAY DIFFRACTIONr_mcbond_it1.4372366
X-RAY DIFFRACTIONr_mcbond_other0.3382115
X-RAY DIFFRACTIONr_mcangle_it1.6053446
X-RAY DIFFRACTIONr_scbond_it2.5364248
X-RAY DIFFRACTIONr_scangle_it3.035179
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 26 -
Rwork0.265 488 -
obs--96.25 %
Refinement TLS params.Method: refined / Origin x: 12.1845 Å / Origin y: 27.5746 Å / Origin z: 3.0117 Å
111213212223313233
T-0.1254 Å20.0048 Å2-0.0004 Å2--0.1532 Å20.0091 Å2---0.0829 Å2
L2.4328 °20.2663 °2-0.2592 °2-1.3522 °20.9049 °2--4.5566 °2
S0.009 Å °-0.0641 Å °0.0172 Å °0.0262 Å °-0.0363 Å °0.0872 Å °-0.0125 Å °-0.0802 Å °0.0273 Å °

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