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- PDB-2a28: Atomic-resolution crystal structure of the second SH3 domain of y... -

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Basic information

Entry
Database: PDB / ID: 2a28
TitleAtomic-resolution crystal structure of the second SH3 domain of yeast Bzz1 determined from a pseudomerohedrally twinned crystal
ComponentsBZZ1 protein
KeywordsSIGNALING PROTEIN / 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 / response to salt stress / actin filament organization / enzyme activator activity ...RND2 GTPase cycle / RHOQ GTPase cycle / actin nucleation / actin cortical patch / regulation of actin filament polymerization / cellular bud neck / mating projection tip / response to salt stress / actin filament organization / enzyme activator activity / 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: 1.07 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 22, 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 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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: BZZ1 protein
B: BZZ1 protein
C: BZZ1 protein
D: BZZ1 protein


Theoretical massNumber of molelcules
Total (without water)23,0734
Polymers23,0734
Non-polymers00
Water7,026390
1
A: BZZ1 protein


Theoretical massNumber of molelcules
Total (without water)5,7681
Polymers5,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BZZ1 protein


Theoretical massNumber of molelcules
Total (without water)5,7681
Polymers5,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BZZ1 protein


Theoretical massNumber of molelcules
Total (without water)5,7681
Polymers5,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BZZ1 protein


Theoretical massNumber of molelcules
Total (without water)5,7681
Polymers5,7681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.840, 51.740, 59.940
Angle α, β, γ (deg.)90.00, 89.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BZZ1 protein


Mass: 5768.271 Da / Num. of mol.: 4 / 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: P38822
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 44 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: ammonium sulfate, pH 8.5, 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: 0.8126 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 7, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8126 Å / Relative weight: 1
ReflectionResolution: 1.07→30 Å / Num. all: 84816 / Num. obs: 84816 / % possible obs: 96 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.2 % / Biso Wilson estimate: 11.9 Å2 / Rsym value: 0.045 / Net I/σ(I): 16.2
Reflection shellResolution: 1.07→1.1 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 6490 / Rsym value: 0.241 / % possible all: 93.1

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.07→20 Å / Num. parameters: 18238 / Num. restraintsaints: 21490 / Isotropic thermal model: ANISOTROPIC REFINEMENT / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The crystal form is twinned by the operator h,-k,-l, twinning fraction 37 %.
RfactorNum. reflection% reflectionSelection details
Rfree0.1663 695 0.8 %RANDOM, SELECTED TAKING INTO ACCOUNT THE TWINNING OPERATOR
Rwork0.1111 ---
all0.1121 84806 --
obs0.1121 84806 95.2 %-
Refine analyzeNum. disordered residues: 4 / Occupancy sum hydrogen: 1428 / Occupancy sum non hydrogen: 2007
Refinement stepCycle: LAST / Resolution: 1.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1634 0 0 390 2024
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0262
X-RAY DIFFRACTIONs_zero_chiral_vol0.101
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.086
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.026
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.052
X-RAY DIFFRACTIONs_approx_iso_adps0.092

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