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- PDB-1zuu: Crystal structure of the yeast Bzz1 first SH3 domain at 0.97-A re... -

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Basic information

Entry
Database: PDB / ID: 1zuu
TitleCrystal structure of the yeast Bzz1 first SH3 domain at 0.97-A resolution
ComponentsBZZ1 protein
KeywordsUNKNOWN FUNCTION / SH3 domain
Function / homology
Function and homology information


RND2 GTPase cycle / RHOQ GTPase cycle / actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / enzyme activator activity / response to salt stress / actin filament organization ...RND2 GTPase cycle / RHOQ GTPase cycle / actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / enzyme activator activity / response to salt stress / actin filament organization / phospholipid binding / endocytosis / plasma membrane / cytoplasm
Similarity search - Function
Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / SH3 Domains / SH3 domain / SH3 type barrels. ...Fes/CIP4, and EFC/F-BAR homology domain / Fes/CIP4 homology domain / FCH domain / F-BAR domain / F-BAR domain profile. / AH/BAR domain superfamily / Variant SH3 domain / 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: 0.97 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 1, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 12, 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 1.4Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: BZZ1 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,4063
Polymers6,3821
Non-polymers242
Water2,396133
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.740, 36.740, 76.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1042-

HOH

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Components

#1: Protein BZZ1 protein


Mass: 6382.083 Da / Num. of mol.: 1 / Fragment: first 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: P38822
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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 Å3/Da / Density % sol: 37.5 %
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: BW7A / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 0.97→20 Å / Num. all: 31881 / Num. obs: 31881 / % possible obs: 100 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 8.7 Å2 / Rsym value: 0.086 / Net I/σ(I): 17.4
Reflection shellResolution: 0.97→1 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.7 / Num. unique all: 2730 / Rsym value: 0.575 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1E6H

1e6h


Resolution: 0.97→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.55 / SU ML: 0.014 / Isotropic thermal model: anisotropic refinement / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R: 0.02 / ESU R Free: 0.021 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1422 1619 5.1 %RANDOM
Rwork0.12309 ---
all0.12407 31881 --
obs0.12407 31881 100 %-
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: 6.294 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 0.97→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms535 0 2 144 681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022546
X-RAY DIFFRACTIONr_bond_other_d0.0010.02491
X-RAY DIFFRACTIONr_angle_refined_deg1.9041.976749
X-RAY DIFFRACTIONr_angle_other_deg0.8631151
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.018572
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.45625.225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.8121599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.19154
X-RAY DIFFRACTIONr_chiral_restr0.1170.286
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02636
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02103
X-RAY DIFFRACTIONr_nbd_refined0.2110.287
X-RAY DIFFRACTIONr_nbd_other0.1860.2461
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2240
X-RAY DIFFRACTIONr_nbtor_other0.0920.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.250.289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.246
X-RAY DIFFRACTIONr_mcbond_it2.0872369
X-RAY DIFFRACTIONr_mcbond_other0.9512142
X-RAY DIFFRACTIONr_mcangle_it2.4733565
X-RAY DIFFRACTIONr_scbond_it3.4354221
X-RAY DIFFRACTIONr_scangle_it4.1855184
X-RAY DIFFRACTIONr_rigid_bond_restr1.68531139
X-RAY DIFFRACTIONr_sphericity_free10.0993146
X-RAY DIFFRACTIONr_sphericity_bonded3.30731026
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.217 113 -
Rwork0.201 2193 -
obs--100 %

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