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- PDB-1neg: Crystal Structure Analysis of N-and C-terminal labeled SH3-domain... -

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Basic information

Entry
Database: PDB / ID: 1neg
TitleCrystal Structure Analysis of N-and C-terminal labeled SH3-domain of alpha-Chicken Spectrin
ComponentsSpectrin alpha chain, brain
KeywordsSTRUCTURAL PROTEIN / SH3-domain fold / five antiparallel beta sheets
Function / homology
Function and homology information


costamere / actin filament capping / 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 / SH3-like domain superfamily / EF-Hand 1, calcium-binding site / Src homology 3 (SH3) domain profile. / SH3 domain / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Roll / Mainly Beta
Similarity search - Domain/homology
AZIDE ION / Spectrin alpha chain, non-erythrocytic 1
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMueller, U. / Buessow, K. / Diehl, A. / Niesen, F.H. / Nyarsik, L. / Heinemann, U.
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2003
Title: Rapid purification and crystal structure analysis of a small protein carrying two terminal affinity tags
Authors: Mueller, U. / Buessow, K. / Diehl, A. / Bartl, F.J. / Niesen, F.H. / Nyarsik, L. / Heinemann, U.
History
DepositionDec 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Dec 21, 2022Group: 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 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE ACCORDING TO THE AUTHOR, THIS IS PART OF A STREP2 TAG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Spectrin alpha chain, brain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,6862
Polymers9,6441
Non-polymers421
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.865, 41.865, 92.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-201-

AZI

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Components

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


Mass: 9643.871 Da / Num. of mol.: 1 / Fragment: SH3-domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Plasmid: pQStrep2 / Production host: Escherichia coli (E. coli) / Strain (production host): scs1 / References: UniProt: P07751
#2: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.44 Å3/Da / Density % sol: 49.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Dioxane, MES, Ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 7, 2000 / Details: mirrors
RadiationMonochromator: Supper mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→31.1 Å / Num. all: 4077 / Num. obs: 3858 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.27 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.109 / Net I/σ(I): 13.05
Reflection shellResolution: 2.3→2.33 Å / Mean I/σ(I) obs: 1.94 / Num. unique all: 130 / Rsym value: 0.461 / % possible all: 95.6
Reflection
*PLUS
Lowest resolution: 31 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.109
Reflection shell
*PLUS
% possible obs: 95.6 % / Rmerge(I) obs: 0.461 / Mean I/σ(I) obs: 1.92

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SHG

1shg


Resolution: 2.3→31.09 Å / Rfactor Rfree error: 0.013 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.249 382 9.9 %RANDOM
Rwork0.2 ---
obs0.2 3858 95.3 %-
all-4077 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.9616 Å2 / ksol: 0.410835 e/Å3
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.5 Å20 Å20 Å2
2--1.5 Å20 Å2
3----3.01 Å2
Refine analyzeLuzzati coordinate error free: 0.35 Å / Luzzati sigma a free: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.3→31.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms547 0 3 46 596
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.462
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.12.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 55 9.6 %
Rwork0.291 517 -
obs--87.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4AZIDE.PARAMAZIDE.TOP
X-RAY DIFFRACTION5PROTEIN_BREAK.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 31.1 Å / % reflection Rfree: 10 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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