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- PDB-2ylf: Crystal structure of the human Spir-1 KIND domain -

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Basic information

Entry
Database: PDB / ID: 2ylf
TitleCrystal structure of the human Spir-1 KIND domain
ComponentsPROTEIN SPIRE HOMOLOG 1
KeywordsACTIN-BINDING PROTEIN / ACTIN POLYMERIZATION / SPIR / KINASE
Function / homology
Function and homology information


formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / positive regulation of double-strand break repair / positive regulation of mitochondrial fission / intracellular transport ...formin-nucleated actin cable assembly / establishment of meiotic spindle localization / polar body extrusion after meiotic divisions / actin filament network formation / actin nucleation / Golgi vesicle transport / cleavage furrow formation / positive regulation of double-strand break repair / positive regulation of mitochondrial fission / intracellular transport / vesicle-mediated transport / actin filament polymerization / cytoplasmic vesicle membrane / protein transport / actin binding / cell cortex / actin cytoskeleton organization / mitochondrial outer membrane / cytoskeleton / innate immune response / perinuclear region of cytoplasm / nucleoplasm / plasma membrane / cytosol
Similarity search - Function
Protein Spire1 / Protein Spire / Kinase non-catalytic C-lobe domain / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / Zinc finger, FYVE/PHD-type / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Protein spire homolog 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZeth, K. / Pechlivanis, M. / Vonrhein, C. / Kerkhoff, E.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Basis of Actin Nucleation Factor Cooperativity: Crystal Structure of the Spir-1 Kinase Non-Catalytic C-Lobe Domain (Kind)Formin-2 Formin Spir Interaction Motif (Fsi) Complex.
Authors: Zeth, K. / Pechlivanis, M. / Samol, A. / Pleiser, S. / Vonrhein, C. / Kerkhoff, E.
History
DepositionJun 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references / Version format compliance
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN SPIRE HOMOLOG 1


Theoretical massNumber of molelcules
Total (without water)25,8391
Polymers25,8391
Non-polymers00
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.914, 65.914, 78.803
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PROTEIN SPIRE HOMOLOG 1 / HUMAN SPIR-1 KIND / SPIR-1


Mass: 25838.787 Da / Num. of mol.: 1 / Fragment: HUMAN SPIR-1 DOMAIN (KIND), RESIDUES 36-236
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q08AE8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 1.91 Å3/Da / Density % sol: 35.69 % / Description: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→33 Å / Num. obs: 11995 / % possible obs: 97.5 % / Observed criterion σ(I): 2.8 / Redundancy: 4 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.1
Reflection shellResolution: 2.05→2.17 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YLE

2yle


Resolution: 2.05→32.96 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.909 / SU B: 11.057 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26339 632 5 %RANDOM
Rwork0.19962 ---
obs0.20283 11995 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.341 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å2-0.25 Å20 Å2
2---0.51 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.05→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 106 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8071.961804
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1065163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.57822.83667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13315238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2861516
X-RAY DIFFRACTIONr_chiral_restr0.1310.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2971.5815
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29221311
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2533518
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2384.5491
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 45 -
Rwork0.282 852 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -28.9336 Å / Origin y: -3.012 Å / Origin z: -8.5915 Å
111213212223313233
T0.0825 Å20.0279 Å2-0.0001 Å2-0.0168 Å20.0014 Å2--0.0608 Å2
L0.5966 °2-0.5764 °20.1408 °2-0.7098 °2-0.1597 °2--0.5898 °2
S-0.0048 Å °-0.0396 Å °0.0467 Å °-0.0066 Å °0.0077 Å °-0.053 Å °-0.0358 Å °-0.017 Å °-0.0028 Å °

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