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- PDB-7s4r: Serial Macromolecular Crystallography at ALBA Synchrotron Light S... -

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Basic information

Entry
Database: PDB / ID: 7s4r
TitleSerial Macromolecular Crystallography at ALBA Synchrotron Light Source - alpha Spectrin-SH3 domain
ComponentsSpectrin alpha chain, non-erythrocytic 1
KeywordsSTRUCTURAL PROTEIN / Serial Crystallography
Function / homology
Function and homology information


actin filament capping / costamere / cortical actin cytoskeleton / cell projection / actin filament binding / cell junction / actin cytoskeleton organization / calmodulin binding / calcium ion binding / plasma membrane
Similarity search - Function
Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / EF-hand domain pair ...Alpha Spectrin, SH3 domain / EF-hand, Ca insensitive / Ca2+ insensitive EF hand / Ca2+ insensitive EF hand / Spectrin repeat / Spectrin repeat / Spectrin/alpha-actinin / Spectrin repeats / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / Src homology 3 domains / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMartin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. ...Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdbury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, R. / Carpena, X.
Funding support2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306
Other government2019-T1BMD-15552
CitationJournal: J.Synchrotron Radiat. / Year: 2022
Title: Serial macromolecular crystallography at ALBA Synchrotron Light Source.
Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / ...Authors: Martin-Garcia, J.M. / Botha, S. / Hu, H. / Jernigan, R. / Castellvi, A. / Lisova, S. / Gil, F. / Calisto, B. / Crespo, I. / Roy-Chowdhury, S. / Grieco, A. / Ketawala, G. / Weierstall, U. / Spence, J. / Fromme, P. / Zatsepin, N. / Boer, D.R. / Carpena, X.
History
DepositionSep 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1May 18, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spectrin alpha chain, non-erythrocytic 1


Theoretical massNumber of molelcules
Total (without water)6,5671
Polymers6,5671
Non-polymers00
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.200, 42.600, 50.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Spectrin alpha chain, non-erythrocytic 1 / Alpha-II spectrin / Fodrin alpha chain


Mass: 6566.512 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P07751
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.82 Å3/Da / Density % sol: 56.35 %
Crystal growTemperature: 277 K / Method: evaporation
Details: Crystals were obtained by applying several concentration/dilution steps with milli-Q water inside standard Amicon Ultra 0.5 ml centrifugal filter (3 kDa cutoff). A crystalline slurry ...Details: Crystals were obtained by applying several concentration/dilution steps with milli-Q water inside standard Amicon Ultra 0.5 ml centrifugal filter (3 kDa cutoff). A crystalline slurry appeared when most citric acid buffer was removed

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→42.6 Å / Num. obs: 4682 / % possible obs: 100 % / Redundancy: 245 % / Biso Wilson estimate: 50.3 Å2 / CC1/2: 0.99 / CC star: 0.9975 / Net I/σ(I): 6.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 57 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 454 / CC1/2: 0.204 / CC star: 0.5817 / % possible all: 100
Serial crystallography sample deliveryDescription: LCP injection / Method: injection
Serial crystallography sample delivery injectionInjector diameter: 5.0E-5 µm
Serial crystallography data reductionFrames failed index: 1145735 / Lattices indexed: 13039

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystFELdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F17

4f17


Resolution: 2.1→32.64 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 8.696 / SU ML: 0.191 / Cross valid method: THROUGHOUT / ESU R: 0.195 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.23989 503 10.9 %RANDOM
Rwork0.19443 ---
obs0.1995 4110 99.14 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.257 Å2
Baniso -1Baniso -2Baniso -3
1-3.56 Å2-0 Å20 Å2
2---3.4 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.1→32.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms463 0 0 5 468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.018472
X-RAY DIFFRACTIONr_bond_other_d0.0010.02462
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.891639
X-RAY DIFFRACTIONr_angle_other_deg0.9982.7511066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.554555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.82124.16724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8621590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg31.516152
X-RAY DIFFRACTIONr_chiral_restr0.0930.271
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02102
X-RAY DIFFRACTIONr_mcbond_it4.4345.824223
X-RAY DIFFRACTIONr_mcbond_other4.3815.788222
X-RAY DIFFRACTIONr_mcangle_it6.88.699277
X-RAY DIFFRACTIONr_mcangle_other6.8228.738278
X-RAY DIFFRACTIONr_scbond_it5.0716.503249
X-RAY DIFFRACTIONr_scbond_other5.0396.431246
X-RAY DIFFRACTIONr_scangle_other7.9149.439361
X-RAY DIFFRACTIONr_long_range_B_refined10.91165.33494
X-RAY DIFFRACTIONr_long_range_B_other10.91665.6495
LS refinement shellResolution: 2.101→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.1607 33 -
Rwork0.1741 264 -
obs--88.13 %

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