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- PDB-5a1k: Crystal structure of calcium-free human adseverin domains A1-A3 -

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Basic information

Entry
Database: PDB / ID: 5a1k
TitleCrystal structure of calcium-free human adseverin domains A1-A3
ComponentsADSEVERIN
KeywordsACTIN-BINDING PROTEIN / ACTIN
Function / homology
Function and homology information


positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / actin filament severing / calcium-ion regulated exocytosis / actin filament capping / barbed-end actin filament capping ...positive regulation of secretion / regulation of chondrocyte differentiation / 1-phosphatidylinositol binding / actin nucleation / positive regulation of actin nucleation / positive regulation of megakaryocyte differentiation / actin filament severing / calcium-ion regulated exocytosis / actin filament capping / barbed-end actin filament capping / cell projection assembly / actin polymerization or depolymerization / podosome / anchoring junction / phosphatidylserine binding / brush border / phosphatidylinositol-4,5-bisphosphate binding / central nervous system development / cell projection / actin filament binding / actin cytoskeleton / actin binding / cell cortex / positive regulation of apoptotic process / negative regulation of cell population proliferation / calcium ion binding / extracellular exosome / cytoplasm
Similarity search - Function
Gelsolin-like domain superfamily / Villin/Gelsolin / Gelsolin homology domain / Severin / Severin / Gelsolin-like domain / Gelsolin repeat / ADF-H/Gelsolin-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsChumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C.
CitationJournal: Nat.Commun. / Year: 2015
Title: Calcium-Controlled Conformational Choreography in the N-Terminal Half of Adseverin.
Authors: Chumnarnsilpa, S. / Robinson, R.C. / Grimes, J.M. / Leyrat, C.
History
DepositionApr 30, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: ADSEVERIN
B: ADSEVERIN


Theoretical massNumber of molelcules
Total (without water)77,6002
Polymers77,6002
Non-polymers00
Water1,928107
1
A: ADSEVERIN


Theoretical massNumber of molelcules
Total (without water)38,8001
Polymers38,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ADSEVERIN


Theoretical massNumber of molelcules
Total (without water)38,8001
Polymers38,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)135.410, 65.250, 105.190
Angle α, β, γ (deg.)90.00, 118.27, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.551, 0.834), (0.008, -1, -0.006), (0.834, 0.01, -0.551)
Vector: -25.024, -12.391, 46.356)

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Components

#1: Protein ADSEVERIN / SCINDERIN


Mass: 38799.824 Da / Num. of mol.: 2 / Fragment: DOMAINS A1-A3, RESIDUES 6-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PSY5 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q9Y6U3
#2: Water ChemComp-HOH / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 47.3 % / Description: NONE
Crystal growDetails: 20 % POLYETHYLENE GLYCOL 3350, 100 MM BIS-TRIS PROPANE PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0033
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0033 Å / Relative weight: 1
ReflectionResolution: 2.9→59.6 Å / Num. obs: 17766 / % possible obs: 98 % / Observed criterion σ(I): 1.5 / Redundancy: 5.5 % / Biso Wilson estimate: 79.21 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.5 % / Rmerge(I) obs: 1.33 / Mean I/σ(I) obs: 1.5 / % possible all: 95

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1D0N RESIDUES 27-370

1d0n


Resolution: 2.9→59.63 Å / Cor.coef. Fo:Fc: 0.8906 / Cor.coef. Fo:Fc free: 0.8939 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.393
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2478 904 5.09 %RANDOM
Rwork0.2396 ---
obs0.24 17745 97.76 %-
Displacement parametersBiso mean: 55.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.7867 Å20 Å2-4.5219 Å2
2--0.2475 Å20 Å2
3----4.0342 Å2
Refine analyzeLuzzati coordinate error obs: 0.499 Å
Refinement stepCycle: LAST / Resolution: 2.9→59.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5414 0 0 107 5521
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085527HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.127448HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1967SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes156HARMONIC2
X-RAY DIFFRACTIONt_gen_planes794HARMONIC5
X-RAY DIFFRACTIONt_it5527HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.3
X-RAY DIFFRACTIONt_other_torsion25.5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion683SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6076SEMIHARMONIC4
LS refinement shellResolution: 2.9→3.08 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3332 155 5.5 %
Rwork0.3024 2663 -
all0.3041 2818 -
obs--97.76 %
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)
12.3365-0.0664-0.21450.5893-0.34880.8591-0.0004-0.00410.01750.00070.0013-0.018-0.0140.0399-0.0009-0.01290.0165-0.0008-0.01010.0073-0.0002-1.25975.195514.4076
21.6810.27620.18220.7865-0.50762.32650.0065-0.05510.00360.0275-0.0014-0.0153-0.0050.038-0.00510.0033-0.00680.00080.01080.0058-0.0066-13.4596-17.822137.3548
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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