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- PDB-7pw0: Crystal structure of the c-Src SH3 domain N112G-N113Y-T114N-E115H... -

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Basic information

Entry
Database: PDB / ID: 7pw0
TitleCrystal structure of the c-Src SH3 domain N112G-N113Y-T114N-E115H mutant
ComponentsIsoform 1 of Proto-oncogene tyrosine-protein kinase Src
KeywordsPROTEIN BINDING / beta barrel / SH3 domain
Function / homologynon-specific protein-tyrosine kinase / Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
Function and homology information
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
Model detailsChimera construction c-Src-Abl SH3 domain
AuthorsCamara-Artigas, A. / Salinas Garcia, M.C.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BIO2006-78020-R Spain
CitationJournal: To be published
Title: The effect of the hinge loops composition in the domain swapping of the SH3 domain
Authors: Camara-Artigas, A. / Salinas Garcia, M.C.
History
DepositionOct 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
B: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
C: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
D: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
E: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
F: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
G: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src
H: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)54,1078
Polymers54,1078
Non-polymers00
Water6,954386
1
A: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Isoform 1 of Proto-oncogene tyrosine-protein kinase Src


Theoretical massNumber of molelcules
Total (without water)6,7631
Polymers6,7631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.259, 93.138, 80.439
Angle α, β, γ (deg.)90.000, 97.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 103 and (name N or name...
21(chain B and ((resid 103 and (name N or name...
31(chain C and ((resid 103 and (name N or name...
41(chain D and ((resid 103 and (name N or name...
51(chain E and ((resid 103 and (name N or name...
61(chain G and ((resid 103 and (name N or name...
71(chain H and (resid 103 through 106 or (resid 108...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLYSLYS(chain A and ((resid 103 and (name N or name...AA10322
12VALVALSERSER(chain A and ((resid 103 and (name N or name...AA83 - 1402 - 59
13VALVALSERSER(chain A and ((resid 103 and (name N or name...AA83 - 1402 - 59
14VALVALSERSER(chain A and ((resid 103 and (name N or name...AA83 - 1402 - 59
15VALVALSERSER(chain A and ((resid 103 and (name N or name...AA83 - 1402 - 59
21LYSLYSLYSLYS(chain B and ((resid 103 and (name N or name...BB10322
22THRTHRSERSER(chain B and ((resid 103 and (name N or name...BB84 - 1403 - 59
23THRTHRSERSER(chain B and ((resid 103 and (name N or name...BB84 - 1403 - 59
24THRTHRSERSER(chain B and ((resid 103 and (name N or name...BB84 - 1403 - 59
25THRTHRSERSER(chain B and ((resid 103 and (name N or name...BB84 - 1403 - 59
31LYSLYSLYSLYS(chain C and ((resid 103 and (name N or name...CC10322
32VALVALSERSER(chain C and ((resid 103 and (name N or name...CC83 - 1402 - 59
33VALVALSERSER(chain C and ((resid 103 and (name N or name...CC83 - 1402 - 59
34VALVALSERSER(chain C and ((resid 103 and (name N or name...CC83 - 1402 - 59
35VALVALSERSER(chain C and ((resid 103 and (name N or name...CC83 - 1402 - 59
41LYSLYSLYSLYS(chain D and ((resid 103 and (name N or name...DD10322
42THRTHRSERSER(chain D and ((resid 103 and (name N or name...DD85 - 1404 - 59
43THRTHRSERSER(chain D and ((resid 103 and (name N or name...DD85 - 1404 - 59
44THRTHRSERSER(chain D and ((resid 103 and (name N or name...DD85 - 1404 - 59
45THRTHRSERSER(chain D and ((resid 103 and (name N or name...DD85 - 1404 - 59
51LYSLYSLYSLYS(chain E and ((resid 103 and (name N or name...EE10322
52GLYGLYASPASP(chain E and ((resid 103 and (name N or name...EE82 - 1411 - 60
53GLYGLYASPASP(chain E and ((resid 103 and (name N or name...EE82 - 1411 - 60
54GLYGLYASPASP(chain E and ((resid 103 and (name N or name...EE82 - 1411 - 60
55GLYGLYASPASP(chain E and ((resid 103 and (name N or name...EE82 - 1411 - 60
61LYSLYSLYSLYS(chain G and ((resid 103 and (name N or name...GG10322
62GLYGLYASPASP(chain G and ((resid 103 and (name N or name...GG82 - 1411 - 60
63GLYGLYASPASP(chain G and ((resid 103 and (name N or name...GG82 - 1411 - 60
64GLYGLYASPASP(chain G and ((resid 103 and (name N or name...GG82 - 1411 - 60
65GLYGLYASPASP(chain G and ((resid 103 and (name N or name...GG82 - 1411 - 60
71LYSLYSGLUGLU(chain H and (resid 103 through 106 or (resid 108...HH103 - 10622 - 25
72LEULEULEULEU(chain H and (resid 103 through 106 or (resid 108...HH10827
73GLYGLYSERSER(chain H and (resid 103 through 106 or (resid 108...HH82 - 1401 - 59
74GLYGLYSERSER(chain H and (resid 103 through 106 or (resid 108...HH82 - 1401 - 59
75GLYGLYSERSER(chain H and (resid 103 through 106 or (resid 108...HH82 - 1401 - 59
76GLYGLYSERSER(chain H and (resid 103 through 106 or (resid 108...HH82 - 1401 - 59

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Components

#1: Protein
Isoform 1 of Proto-oncogene tyrosine-protein kinase Src / Proto-oncogene c-Src / pp60c-src / p60-Src


Mass: 6763.364 Da / Num. of mol.: 8 / Mutation: N112G, N113Y, T114N, E115H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: SRC / Plasmid: pHTP1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00523-1, non-specific protein-tyrosine kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.56 Å3/Da / Density % sol: 51.93 % / Mosaicity: 0.22 °
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.8 M ammonium sulfate, 5% PEG 300, 10% glycerol, 40mM LiCl, 0.1M AcONa

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.97924 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 1.7→19.95 Å / Num. obs: 59211 / % possible obs: 99 % / Redundancy: 4.3 % / Biso Wilson estimate: 23.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.04 / Rrim(I) all: 0.085 / Net I/σ(I): 9.4 / Num. measured all: 255084 / Scaling rejects: 94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.734.21.3071307931160.5420.7211.4971.198.7
9-19.9540.03814993750.9980.0210.04427.187.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.7data scaling
PHASERphasing
PHENIX1.19.1refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JZ4

4jz4


Resolution: 1.7→19.95 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0.01 / Phase error: 30.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 5685 4.95 %
Rwork0.2083 109274 -
obs0.2093 114959 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.88 Å2 / Biso mean: 36.4486 Å2 / Biso min: 18.43 Å2
Refinement stepCycle: final / Resolution: 1.7→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3624 0 0 386 4010
Biso mean---39.37 -
Num. residues----465
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A665X-RAY DIFFRACTION12.005TORSIONAL
12B665X-RAY DIFFRACTION12.005TORSIONAL
13C665X-RAY DIFFRACTION12.005TORSIONAL
14D665X-RAY DIFFRACTION12.005TORSIONAL
15E665X-RAY DIFFRACTION12.005TORSIONAL
16G665X-RAY DIFFRACTION12.005TORSIONAL
17H665X-RAY DIFFRACTION12.005TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.720.39711930.42383538373196
1.72-1.740.45221820.396737033885100
1.74-1.760.37892080.36963794400299
1.76-1.780.36221840.362137243908100
1.78-1.810.38691980.345836373835100
1.81-1.830.32661870.32293758394599
1.83-1.860.32621560.29393819397599
1.86-1.890.30841920.29743649384199
1.89-1.910.31661980.28633685388399
1.91-1.950.29742160.26983700391699
1.95-1.980.25042010.24513741394299
1.98-2.020.24131660.22523713387999
2.02-2.050.26412140.22523712392699
2.05-2.10.22592150.22453648386399
2.1-2.140.21551750.20953696387199
2.14-2.190.20331730.1943784395799
2.19-2.250.21891970.19913585378298
2.25-2.310.23451920.20493707389998
2.31-2.370.21721900.19553672386298
2.37-2.450.2251990.19893676387599
2.45-2.540.27761970.21953639383698
2.54-2.640.25091960.20913691388798
2.64-2.760.27651830.20813588377197
2.76-2.90.28141670.21353627379496
2.9-3.090.24141800.2053335351589
3.09-3.320.23021870.19313525371294
3.32-3.660.16371850.17613520370594
3.66-4.180.16191790.15023473365293
4.18-5.250.14831790.14853480365993
5.25-19.950.21681960.21493455365193

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