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- PDB-5bvr: Actin binding domain of alpha-actinin from Schizosaccharomyces pombe -

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Basic information

Entry
Database: PDB / ID: 5bvr
TitleActin binding domain of alpha-actinin from Schizosaccharomyces pombe
ComponentsAlpha-actinin-like protein 1
KeywordsCELL CYCLE / alpha-actinin actin binding Schizosaccharomyces pombe / cell division
Function / homology
Function and homology information


RHOD GTPase cycle / actin lateral binding / actomyosin contractile ring assembly actin filament bundle convergence / RHOV GTPase cycle / Platelet degranulation / COPI-mediated anterograde transport / mitotic actomyosin contractile ring / RHOU GTPase cycle / Neutrophil degranulation / actomyosin contractile ring ...RHOD GTPase cycle / actin lateral binding / actomyosin contractile ring assembly actin filament bundle convergence / RHOV GTPase cycle / Platelet degranulation / COPI-mediated anterograde transport / mitotic actomyosin contractile ring / RHOU GTPase cycle / Neutrophil degranulation / actomyosin contractile ring / actin crosslink formation / cortical actin cytoskeleton / actin filament bundle / actin filament bundle assembly / cell projection / actin filament binding / protein-macromolecule adaptor activity / actin cytoskeleton organization
Similarity search - Function
Calponin-like domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / Ca2+ insensitive EF hand / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain ...Calponin-like domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Actin-binding Protein, T-fimbrin; domain 1 / Ca2+ insensitive EF hand / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / EF-hand domain pair / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-actinin-like protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å
AuthorsPersson, K. / Backman, L. / Addario, B.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Car trygger foundation Sweden
CitationJournal: Peerj / Year: 2016
Title: Characterisation of Schizosaccharomyces pombe alpha-actinin.
Authors: Addario, B. / Sandblad, L. / Persson, K. / Backman, L.
History
DepositionJun 5, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-actinin-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4884
Polymers27,2921
Non-polymers1963
Water5,170287
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area290 Å2
ΔGint-86 kcal/mol
Surface area11510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.537, 79.468, 91.933
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-actinin-like protein 1


Mass: 27292.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The first residues, GS, originate from the cloning vector.
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: ain1, SPAC15A10.08 / Plasmid: pET19-b / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: O13728
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.3 Å3/Da / Density % sol: 46.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 18% PEG 6000, 5 mM ZnCl2 / PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.46→45.97 Å / Num. obs: 309226 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 14.6
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 2.1 / % possible all: 98.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EYI

2eyi


Resolution: 1.46→45.966 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1866 1999 4.6 %Random
Rwork0.1579 41455 --
obs0.1592 43454 99.5 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 97.89 Å2 / Biso mean: 28.7124 Å2 / Biso min: 11.49 Å2
Refinement stepCycle: final / Resolution: 1.46→45.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1870 0 3 287 2160
Biso mean--20.48 37.48 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091920
X-RAY DIFFRACTIONf_angle_d1.152601
X-RAY DIFFRACTIONf_chiral_restr0.069291
X-RAY DIFFRACTIONf_plane_restr0.006334
X-RAY DIFFRACTIONf_dihedral_angle_d12.021728
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.46-1.49510.27081350.26972794X-RAY DIFFRACTION97
1.4951-1.53550.30951410.23882945X-RAY DIFFRACTION100
1.5355-1.58070.23471410.21682903X-RAY DIFFRACTION100
1.5807-1.63180.20951400.18762924X-RAY DIFFRACTION100
1.6318-1.69010.22961420.18742938X-RAY DIFFRACTION99
1.6901-1.75770.21741420.17382952X-RAY DIFFRACTION100
1.7577-1.83770.20911420.1652933X-RAY DIFFRACTION100
1.8377-1.93460.18151410.15632940X-RAY DIFFRACTION100
1.9346-2.05590.20191440.14932963X-RAY DIFFRACTION100
2.0559-2.21460.19651430.14652979X-RAY DIFFRACTION100
2.2146-2.43740.18981440.14212978X-RAY DIFFRACTION100
2.4374-2.79010.19241460.14523019X-RAY DIFFRACTION100
2.7901-3.5150.14671440.15163007X-RAY DIFFRACTION100
3.515-45.9890.17311540.15213180X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.062-0.03120.59430.9966-0.31231.74980.0578-0.0178-0.0393-0.0664-0.03960.08730.092-0.062800.180.0028-0.0110.1507-0.00760.1543-10.1119-8.78856.7896
21.3812-0.06270.5881.0038-0.18691.7770.07-0.152-0.16360.02440.0012-0.02350.068-0.05570.00270.1248-0.0163-0.0090.12770.03330.1573-2.3753-15.820332.0896
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:119)A6 - 119
2X-RAY DIFFRACTION2(chain A and resid 120:234)A120 - 234

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