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- PDB-5nxj: SH3 domain from Mouse cortactin (P 1 21 1 crystal form) -

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Basic information

Entry
Database: PDB / ID: 5nxj
TitleSH3 domain from Mouse cortactin (P 1 21 1 crystal form)
ComponentsSrc substrate cortactin
KeywordsPROTEIN BINDING / SH3 domain / cortactin / signaling / cancer / invadopodium
Function / homology
Function and homology information


lamellipodium organization / mitotic spindle midzone / regulation of mitophagy / profilin binding / positive regulation of smooth muscle contraction / substrate-dependent cell migration, cell extension / focal adhesion assembly / dendritic spine maintenance / podosome / regulation of axon extension ...lamellipodium organization / mitotic spindle midzone / regulation of mitophagy / profilin binding / positive regulation of smooth muscle contraction / substrate-dependent cell migration, cell extension / focal adhesion assembly / dendritic spine maintenance / podosome / regulation of axon extension / positive regulation of actin filament polymerization / cortical cytoskeleton / clathrin-coated pit / extrinsic apoptotic signaling pathway / ruffle / voltage-gated potassium channel complex / receptor-mediated endocytosis / neuron projection morphogenesis / negative regulation of extrinsic apoptotic signaling pathway / actin filament / intracellular protein transport / cell motility / cell junction / lamellipodium / actin cytoskeleton organization / cell cortex / dendritic spine / focal adhesion / endoplasmic reticulum / Golgi apparatus / cytosol / cytoplasm
Similarity search - Function
Hs1/Cortactin / Repeat in HS1/Cortactin / Cortactin repeat profile. / Cortactin, SH3 domain / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. ...Hs1/Cortactin / Repeat in HS1/Cortactin / Cortactin repeat profile. / Cortactin, SH3 domain / Variant SH3 domain / SH3 Domains / Src homology 3 domains / SH3 type barrels. / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Src substrate cortactin
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 Å
AuthorsTwafra, S. / Dessau, M.
CitationJournal: To Be Published
Title: SH3 domain from Mouse cortactin (P 1 21 1 crystal form)
Authors: Twafra, S. / Gil-Henn, H. / Dessau, M.
History
DepositionMay 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Src substrate cortactin
B: Src substrate cortactin
C: Src substrate cortactin
D: Src substrate cortactin
E: Src substrate cortactin
F: Src substrate cortactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9358
Polymers40,8156
Non-polymers1202
Water2,432135
1
A: Src substrate cortactin


Theoretical massNumber of molelcules
Total (without water)6,8031
Polymers6,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Src substrate cortactin


Theoretical massNumber of molelcules
Total (without water)6,8031
Polymers6,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Src substrate cortactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8632
Polymers6,8031
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Src substrate cortactin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8632
Polymers6,8031
Non-polymers601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Src substrate cortactin


Theoretical massNumber of molelcules
Total (without water)6,8031
Polymers6,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Src substrate cortactin


Theoretical massNumber of molelcules
Total (without water)6,8031
Polymers6,8031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.340, 80.080, 61.120
Angle α, β, γ (deg.)90.000, 99.640, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Src substrate cortactin


Mass: 6802.532 Da / Num. of mol.: 6 / Fragment: SH3 domain, UNP Residues 490-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cttn, Ems1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q60598
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 49.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.2 M (NH4)2SO4, 0.1 M sodium citrate pH 5, 3% 2_propanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976251 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976251 Å / Relative weight: 1
ReflectionResolution: 2.28→60.257 Å / Num. obs: 17678 / % possible obs: 98.4 % / Redundancy: 3.368 % / Biso Wilson estimate: 30.11 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.163 / Rrim(I) all: 0.194 / Χ2: 0.94 / Net I/σ(I): 6.16 / Num. measured all: 59539
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.28-2.343.3520.6771.874381132313070.4890.80898.8
2.34-2.413.430.6332.084418129512880.550.7599.5
2.41-2.483.4270.562.324160123112140.6450.66598.6
2.48-2.553.4010.5372.494139122312170.6440.63899.5
2.55-2.643.320.4842.723844118511580.720.57897.7
2.64-2.733.10.4292.913398114010960.750.5296.1
2.73-2.833.50.353.753756109710730.8870.41497.8
2.83-2.953.4390.3064.473704107910770.9010.36499.8
2.95-3.083.4710.2515.41345410069950.9280.29898.9
3.08-3.233.4140.2046.5733359859770.9630.24299.2
3.23-3.43.3550.1627.8230509249090.9740.19398.4
3.4-3.613.1680.1328.7526588828390.9740.15995.1
3.61-3.863.5380.10710.8728768178130.9870.12699.5
3.86-4.173.4930.08112.9826627717620.9930.09598.8
4.17-4.563.4060.07313.8824327157140.9920.08799.9
4.56-5.13.190.08212.1619816386210.9910.09897.3
5.1-5.893.2780.08711.7318425755620.9910.10497.7
5.89-7.223.4240.08712.116304844760.9940.10398.3
7.22-10.213.0960.06913.2511643793760.9950.08399.2
10.21-60.2573.2110.05514.396552112040.9970.06696.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1X69

1x69


Resolution: 2.282→60.257 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2484 863 4.89 %
Rwork0.1978 16800 -
obs0.2002 17663 98.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 144.53 Å2 / Biso mean: 40.7326 Å2 / Biso min: 15.75 Å2
Refinement stepCycle: final / Resolution: 2.282→60.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2874 0 8 135 3017
Biso mean--52.28 35.02 -
Num. residues----360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042988
X-RAY DIFFRACTIONf_angle_d0.6954062
X-RAY DIFFRACTIONf_chiral_restr0.05410
X-RAY DIFFRACTIONf_plane_restr0.003540
X-RAY DIFFRACTIONf_dihedral_angle_d19.7071722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.282-2.4250.38911460.30272806295299
2.425-2.61220.2981500.27392772292299
2.6122-2.87510.27971430.24122758290197
2.8751-3.29110.24351240.20272846297099
3.2911-4.14630.22131510.15382778292998
4.1463-60.27850.20791490.1632840298998
Refinement TLS params.Method: refined / Origin x: -17.9444 Å / Origin y: -11.1434 Å / Origin z: -14.7689 Å
111213212223313233
T0.1955 Å20.0161 Å2-0.002 Å2-0.1935 Å2-0.0035 Å2--0.1779 Å2
L0.5101 °20.0223 °20.0271 °2-0.1327 °2-0.0546 °2--0.1411 °2
S-0.0017 Å °-0.0179 Å °-0.0024 Å °0.0065 Å °0.0079 Å °-0.0189 Å °-0.0371 Å °-0.0078 Å °0.0002 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 61
2X-RAY DIFFRACTION1allB2 - 61
3X-RAY DIFFRACTION1allC2 - 61
4X-RAY DIFFRACTION1allD2 - 61
5X-RAY DIFFRACTION1allE2 - 61
6X-RAY DIFFRACTION1allF2 - 61
7X-RAY DIFFRACTION1allS1 - 138
8X-RAY DIFFRACTION1allG1 - 2

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