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- PDB-3pp5: High-resolution structure of the trimeric Scar/WAVE complex precu... -

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Basic information

Entry
Database: PDB / ID: 3pp5
TitleHigh-resolution structure of the trimeric Scar/WAVE complex precursor Brk1
ComponentsBrk1
KeywordsSTRUCTURAL PROTEIN / triple coiled-coil / precursor of the Scar-WAVE complex / Abi / Scar
Function / homology
Function and homology information


pseudopodium assembly / SCAR complex / cell pole / regulation of actin polymerization or depolymerization / filopodium tip / cell leading edge / pseudopodium / actin filament organization / cell motility / cell-cell junction ...pseudopodium assembly / SCAR complex / cell pole / regulation of actin polymerization or depolymerization / filopodium tip / cell leading edge / pseudopodium / actin filament organization / cell motility / cell-cell junction / cytoskeleton / protein-containing complex binding / identical protein binding
Similarity search - Function
Protein BRICK1 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLinkner, J. / Witte, G. / Curth, U. / Faix, J.
CitationJournal: Plos One / Year: 2011
Title: High-resolution X-ray structure of the trimeric Scar/WAVE-complex precursor Brk1.
Authors: Linkner, J. / Witte, G. / Stradal, T. / Curth, U. / Faix, J.
History
DepositionNov 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

Deposited unit
A: Brk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9365
Polymers8,6201
Non-polymers3174
Water1,928107
1
A: Brk1
hetero molecules

A: Brk1
hetero molecules

A: Brk1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,80915
Polymers25,8593
Non-polymers95012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area8200 Å2
ΔGint-179 kcal/mol
Surface area13130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.140, 39.140, 118.190
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Brk1 / / Protein BRICK1


Mass: 8619.741 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: brk1, DDB_G0279175, hspc300 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) rosetta / References: UniProt: Q54X65
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 40% (v/v) MPD, 0.2 M CaCl2, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA11.0722
SYNCHROTRONESRF ID23-220.8726
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDAug 15, 2009
MARMOSAIC 225 mm CCD2CCDJul 10, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Bartels Monochromator (Si 111)SINGLE WAVELENGTHMx-ray1
2Silicon 111 crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07221
20.87261
ReflectionResolution: 1.5→20 Å / Num. all: 16414 / Num. obs: 16181 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 12.5 % / Biso Wilson estimate: 22.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 30.4
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 12.09 % / Mean I/σ(I) obs: 8.95 / Rsym value: 0.27 / % possible all: 97.4

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SHELX(anomalous dataset)model building
ARP/wARPmodel building
PHENIX(phenix.refine: 1.6_289)refinement
XDSdata reduction
XSCALEdata scaling
SHELX(anomalous dataset)phasing
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT / Resolution: 1.5→19.389 Å / SU ML: 0.14 / σ(F): 2.04 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1817 806 4.99 %random
Rwork0.1589 ---
obs0.1601 16144 98.65 %-
all-16414 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.614 Å2 / ksol: 0.384 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.4388 Å2-0 Å2-0 Å2
2--2.4388 Å2-0 Å2
3----4.8777 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 18 107 661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013621
X-RAY DIFFRACTIONf_angle_d1.245843
X-RAY DIFFRACTIONf_dihedral_angle_d15.787248
X-RAY DIFFRACTIONf_chiral_restr0.07494
X-RAY DIFFRACTIONf_plane_restr0.005108
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.5940.16731310.15672504X-RAY DIFFRACTION98
1.594-1.7170.17461350.1512559X-RAY DIFFRACTION99
1.717-1.88970.18381350.16182575X-RAY DIFFRACTION99
1.8897-2.16280.19411350.14242568X-RAY DIFFRACTION99
2.1628-2.72370.16941360.14612582X-RAY DIFFRACTION99
2.7237-19.39060.18051340.16632550X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: 18.0149 Å / Origin y: -6.0166 Å / Origin z: 17.0839 Å
111213212223313233
T0.08 Å2-0.0017 Å2-0.0031 Å2-0.0661 Å2-0.0035 Å2--0.0801 Å2
L-0.0514 °2-0.0002 °2-0.2194 °2-0.2143 °20.4286 °2--0.3073 °2
S0.001 Å °0.0128 Å °0.0184 Å °0.014 Å °0.041 Å °-0.0281 Å °-0.0625 Å °-0.0246 Å °0.0073 Å °
Refinement TLS groupSelection details: All

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