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- PDB-1wdx: Yeast BBC1 SH3 domain, triclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 1wdx
TitleYeast BBC1 SH3 domain, triclinic crystal form
ComponentsMyosin tail region-interacting protein MTI1
KeywordsCONTRACTILE PROTEIN / SH3 domain
Function / homology
Function and homology information


myosin I binding / actin cortical patch / lamellipodium assembly / cytoskeleton organization / guanyl-nucleotide exchange factor activity / lamellipodium / actin cytoskeleton organization / nucleolus
Similarity search - Function
Mti1, 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
Myosin tail region-interacting protein MTI1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsWilmanns, M. / Consani Textor, L. / Kursula, P. / Kursula, I. / Lehmann, F. / Song, Y.H.
CitationJournal: To be Published
Title: Crystal structure of Yeast BBC1 SH3 domain, triclinic crystal form
Authors: Wilmanns, M. / Consani Textor, L. / Kursula, P. / Kursula, I. / Lehmann, F. / Song, Y.H.
History
DepositionMay 19, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2005Provider: 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin tail region-interacting protein MTI1
B: Myosin tail region-interacting protein MTI1
C: Myosin tail region-interacting protein MTI1
D: Myosin tail region-interacting protein MTI1


Theoretical massNumber of molelcules
Total (without water)31,5144
Polymers31,5144
Non-polymers00
Water28816
1
A: Myosin tail region-interacting protein MTI1


Theoretical massNumber of molelcules
Total (without water)7,8791
Polymers7,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myosin tail region-interacting protein MTI1


Theoretical massNumber of molelcules
Total (without water)7,8791
Polymers7,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Myosin tail region-interacting protein MTI1


Theoretical massNumber of molelcules
Total (without water)7,8791
Polymers7,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Myosin tail region-interacting protein MTI1


Theoretical massNumber of molelcules
Total (without water)7,8791
Polymers7,8791
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.730, 44.770, 51.120
Angle α, β, γ (deg.)89.83, 83.37, 85.41
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 4 / Auth seq-ID: 5 - 67 / Label seq-ID: 5 - 67

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Myosin tail region-interacting protein MTI1 / BBC1 protein


Mass: 7878.516 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: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: P47068
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.1 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 3.2M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 28, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 11615 / Num. obs: 11615 / % possible obs: 90.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 1.7 % / Biso Wilson estimate: 18 Å2 / Rsym value: 0.144 / Net I/σ(I): 3.9
Reflection shellResolution: 2.2→2.4 Å / Redundancy: 1.7 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 2707 / Rsym value: 0.291 / % possible all: 92.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: atomic-resolution structure of yeast bbc1 SH3 domain

Resolution: 2.5→10 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.729 / SU B: 16.625 / SU ML: 0.377 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.456 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32595 388 5 %RANDOM
Rwork0.26286 ---
all0.26594 7751 --
obs0.26594 7751 90.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.038 Å2
Baniso -1Baniso -2Baniso -3
1-2.26 Å2-0.31 Å2-0.2 Å2
2---2.06 Å2-0.66 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 0 16 2084
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222128
X-RAY DIFFRACTIONr_bond_other_d0.0020.021756
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9342892
X-RAY DIFFRACTIONr_angle_other_deg0.70534136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1695248
X-RAY DIFFRACTIONr_chiral_restr0.0590.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022404
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02440
X-RAY DIFFRACTIONr_nbd_refined0.1580.2417
X-RAY DIFFRACTIONr_nbd_other0.1950.22132
X-RAY DIFFRACTIONr_nbtor_other0.0810.21235
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2330.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1980.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.25
X-RAY DIFFRACTIONr_mcbond_it0.56631260
X-RAY DIFFRACTIONr_mcangle_it0.94242052
X-RAY DIFFRACTIONr_scbond_it0.6544868
X-RAY DIFFRACTIONr_scangle_it0.9735840
Refine LS restraints NCS

Ens-ID: 1 / Number: 956 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.350.5
2Bmedium positional0.370.5
3Cmedium positional0.420.5
4Dmedium positional0.460.5
1Amedium thermal0.292
2Bmedium thermal0.282
3Cmedium thermal0.272
4Dmedium thermal0.232
LS refinement shellResolution: 2.5→2.561 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.387 28
Rwork0.281 532

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