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- PDB-1ux5: Crystal Structures of a Formin Homology-2 domain reveal a flexibl... -

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Basic information

Entry
Database: PDB / ID: 1ux5
TitleCrystal Structures of a Formin Homology-2 domain reveal a flexibly tethered dimer architecture
ComponentsBNI1 PROTEIN
KeywordsSTRUCTURAL PROTEIN / FH2 ACTIN CYTOSKELETON
Function / homology
Function and homology information


polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / vesicle targeting / mitotic actomyosin contractile ring assembly / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site / cellular bud tip ...polarisome / formin-nucleated actin cable assembly / budding cell apical bud growth / vesicle targeting / mitotic actomyosin contractile ring assembly / prospore membrane / establishment or maintenance of actin cytoskeleton polarity / actin nucleation / incipient cellular bud site / cellular bud tip / profilin binding / cellular bud neck / mating projection tip / barbed-end actin filament capping / establishment of cell polarity / cell division site / establishment of mitotic spindle orientation / actin filament bundle assembly / actin filament / regulation of actin cytoskeleton organization / small GTPase binding / regulation of protein localization / actin binding / identical protein binding / plasma membrane
Similarity search - Function
Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #50 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Formin, FH2 domain / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain ...Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 - #50 / Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 / Formin, FH2 domain / Diaphanous autoregulatory (DAD) domain / Diaphanous autoregulatory domain (DAD) profile. / Formin, FH3 domain / Formin, GTPase-binding domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Diaphanous FH3 Domain / Diaphanous GTPase-binding Domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain / Rho GTPase-binding/formin homology 3 (GBD/FH3) domain profile. / Formin, FH2 domain / Formin, FH2 domain superfamily / Formin Homology 2 Domain / Formin homology-2 (FH2) domain profile. / Formin Homology 2 Domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix non-globular / Special / Armadillo-like helical / Armadillo-type fold / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsXu, Y. / Moseley, J.B. / Sagot, I. / Poy, F. / Pellman, D. / Goode, B.L. / Eck, M.J.
Citation
Journal: Cell(Cambridge,Mass.) / Year: 2004
Title: Crystal Structures of a Formin Homology-2 Domain Reveal a Tethered Dimer Architecture
Authors: Xu, Y. / Moseley, J.B. / Sagot, I. / Poy, F. / Pellman, D. / Goode, B.L. / Eck, M.J.
#1: Journal: Nat.Cell Biol. / Year: 2002
Title: Yeast Formins Regulate Cell Polarity by Controlling the Assembly of Actin Cables
Authors: Sagot, I. / Klee, S.K. / Pellman, D.
History
DepositionFeb 19, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BNI1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)47,3961
Polymers47,3961
Non-polymers00
Water55831
1
A: BNI1 PROTEIN

A: BNI1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)94,7922
Polymers94,7922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)101.400, 101.400, 265.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsBIOLOGICAL_UNIT: INTERACTS WITH PROFILIN AND ACTINAT THE FH1 AND FH2 DOMAINS RESPECTIVELY.

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Components

#1: Protein BNI1 PROTEIN / FORMIN / SYNTHETIC LETHAL 39


Mass: 47395.859 Da / Num. of mol.: 1 / Fragment: FH2 DOMAIN, RESIDUES 1350-1760
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P41832
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Compound detailsORGANIZES MICROTUBULES BY MEDIATING SPINDLE POSITIONING AND MOVEMENT IN THE BUDDING PROCESS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.16 Å3/Da / Density % sol: 70 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP AGAINST A WELL CONTAINING 16% ETHYLENE GLYCOL, pH 7.50
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
22.5 mMPCMBS1drop
316 %ethylene glycol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONCHESS A110.916, 0.936
SYNCHROTRONCHESS F121.007
SYNCHROTRONCHESS F231.009
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2x-ray1
3x-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9161
20.9361
31.0071
41.0091
ReflectionResolution: 2.5→30 Å / Num. obs: 49995 / % possible obs: 90 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 12.9
Reflection
*PLUS
Highest resolution: 2.5 Å / % possible obs: 94.5 % / Num. measured all: 154481 / Rmerge(I) obs: 0.087
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 90 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.5→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -7 %RANDOM
Rwork0.207 ---
obs0.207 34619 65.5 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 0 31 3366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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