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- PDB-3i9q: Crystal Structure of the triple mutant S19G-P20D-R21S of alpha sp... -

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Basic information

Entry
Database: PDB / ID: 3i9q
TitleCrystal Structure of the triple mutant S19G-P20D-R21S of alpha spectrin SH3 domain
ComponentsSpectrin alpha chain
KeywordsSTRUCTURAL PROTEIN / SH3-like barrel / Actin capping / Actin-binding / Calmodulin-binding / Cytoskeleton / Phosphoprotein / SH3 domain
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 Domains / SH3 domain ...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 Domains / SH3 domain / EF-hand domain pair / EF-hand, calcium binding motif / SH3 type barrels. / Src homology 3 domains / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand domain / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / Resolution: 1.45 Å
AuthorsCamara-Artigas, A. / Gavira, J.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: The effect of a proline residue on the rate of growth and the space group of alpha-spectrin SH3-domain crystals.
Authors: Camara-Artigas, A. / Andujar-Sanchez, M. / Ortiz-Salmeron, E. / Cuadri, C. / Casares, S.
History
DepositionJul 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 19, 2013Group: Database references
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7102
Polymers6,6141
Non-polymers961
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.231, 42.231, 93.655
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Spectrin alpha chain / Spectrin / non-erythroid alpha chain / Fodrin alpha chain


Mass: 6613.523 Da / Num. of mol.: 1 / Fragment: SH3 domain (UNP residues 969 to 1025) / Mutation: S19G, P20D, R21S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SPTAN1, SPTA2 / Plasmid: pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P07751
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 3.16 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2 M ammonium sulphate, 0.1 M MES pH 6.5, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 3, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→20 Å / Num. all: 15848 / Num. obs: 15182 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.4 % / Biso Wilson estimate: 22.168 Å2 / Rmerge(I) obs: 0.063 / Χ2: 1.089 / Net I/σ(I): 19.3
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 6.82 / Num. unique all: 1552 / Χ2: 1.178 / % possible all: 99.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1SHG

1shg


Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.932 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.382 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.072 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.243 756 5 %RANDOM
Rwork0.232 ---
obs0.232 15041 95.59 %-
all-15848 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.4 Å2 / Biso mean: 14.129 Å2 / Biso min: 4.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2--0.15 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.45→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms465 0 5 58 528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022477
X-RAY DIFFRACTIONr_angle_refined_deg2.3711.978644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.143556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.47126.36422
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2231592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.431151
X-RAY DIFFRACTIONr_chiral_restr0.1550.271
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02344
X-RAY DIFFRACTIONr_mcbond_it2.0741.5282
X-RAY DIFFRACTIONr_mcangle_it2.9172454
X-RAY DIFFRACTIONr_scbond_it4.323195
X-RAY DIFFRACTIONr_scangle_it5.8584.5190
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 66 -
Rwork0.357 1062 -
all-1128 -
obs--99.91 %
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)
112.76283.637.86513.98123.14721.05830.2538-0.3169-0.24930.1834-0.0871-0.82790.27540.7536-0.16660.12940.01010.03580.0743-0.00860.1106-7.491-0.3910.035
25.18091.07970.822210.03730.19947.008-0.3243-0.4996-0.0045-0.0589-0.37561.3209-0.148-1.02840.69980.08980.0439-0.02410.2101-0.14680.2615-21.132-7.3297.741
31.4873-1.31740.463110.4181.24732.4253-0.0232-0.01680.09240.0685-0.15660.0029-0.0798-0.12440.17980.1133-0.0096-0.00480.0673-0.00910.0682-11.211-7.91810.014
413.76623.4915-2.46425.5548.861414.3933-0.18990.28370.3363-0.3754-0.58430.5912-0.5483-0.66570.77420.16420.03050.01450.1467-0.09860.1287-18.468-2.70717.808
53.41010.3132-1.36129.13163.19256.8589-0.0320.07260.0794-0.5282-0.026-0.4613-0.47040.21930.05790.17970.0242-0.00660.0745-0.00550.0879-10.659-6.2685.884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 11
2X-RAY DIFFRACTION2A12 - 26
3X-RAY DIFFRACTION3A27 - 45
4X-RAY DIFFRACTION4A46 - 50
5X-RAY DIFFRACTION5A51 - 62

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