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- PDB-6les: 3D domain-swapped dimer of the maltose-binding protein fused to a... -

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Basic information

Entry
Database: PDB / ID: 6les
Title3D domain-swapped dimer of the maltose-binding protein fused to a fragment of the focal adhesion kinase
ComponentsMaltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
KeywordsSUGAR BINDING PROTEIN / maltose binding protein / domain-swapping / arm exchange / folding / passenger protein / surface entropy reduction / fixed-arm carrier / dimer / FAK / apo-protein
Function / homology
Function and homology information


netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / JUN kinase binding / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling ...netrin-activated signaling pathway / regulation of substrate adhesion-dependent cell spreading / regulation of endothelial cell migration / regulation of epithelial cell migration / detection of muscle stretch / JUN kinase binding / signal complex assembly / positive regulation of ubiquitin-dependent protein catabolic process / positive regulation of macrophage proliferation / DCC mediated attractive signaling / Signal regulatory protein family interactions / positive regulation of fibroblast migration / regulation of GTPase activity / MET activates PTK2 signaling / growth hormone receptor signaling pathway / regulation of focal adhesion assembly / negative regulation of cell-cell adhesion / regulation of osteoblast differentiation / positive regulation of wound healing / p130Cas linkage to MAPK signaling for integrins / Apoptotic cleavage of cellular proteins / positive regulation of macrophage chemotaxis / detection of maltose stimulus / regulation of cytoskeleton organization / regulation of cell adhesion mediated by integrin / establishment of cell polarity / maltose transport complex / Fc-gamma receptor signaling pathway involved in phagocytosis / regulation of protein phosphorylation / vascular endothelial cell response to oscillatory fluid shear stress / carbohydrate transport / GRB2:SOS provides linkage to MAPK signaling for Integrins / positive regulation of protein kinase activity / negative regulation of anoikis / positive regulation of epithelial cell migration / carbohydrate transmembrane transporter activity / maltose binding / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / RHO GTPases Activate WASPs and WAVEs / maltose transport / maltodextrin transmembrane transport / ephrin receptor signaling pathway / vascular endothelial growth factor receptor signaling pathway / positive regulation of epithelial to mesenchymal transition / regulation of cell adhesion / heart morphogenesis / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / stress fiber / Integrin signaling / EPHB-mediated forward signaling / NCAM signaling for neurite out-growth / SH2 domain binding / transforming growth factor beta receptor signaling pathway / ATP-binding cassette (ABC) transporter complex / protein tyrosine phosphatase activity / axon guidance / peptidyl-tyrosine phosphorylation / molecular function activator activity / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / placenta development / integrin-mediated signaling pathway / cell chemotaxis / non-membrane spanning protein tyrosine kinase activity / FCGR3A-mediated phagocytosis / non-specific protein-tyrosine kinase / cell motility / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / integrin binding / epidermal growth factor receptor signaling pathway / positive regulation of protein phosphorylation / cell migration / regulation of cell shape / regulation of cell population proliferation / outer membrane-bounded periplasmic space / protein autophosphorylation / actin binding / RAF/MAP kinase cascade / protein tyrosine kinase activity / angiogenesis / cell cortex / protein phosphatase binding / cytoskeleton / periplasmic space / Extra-nuclear estrogen signaling / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cilium / positive regulation of cell migration / ciliary basal body / focal adhesion / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / DNA damage response / centrosome / protein kinase binding / negative regulation of apoptotic process / perinuclear region of cytoplasm / ATP binding / nucleus / membrane
Similarity search - Function
Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain ...Focal adhesion kinase, targeting (FAT) domain / Focal adhesion kinase, targeting (FAT) domain superfamily / Focal adhesion kinase, N-terminal / FAK1/PYK2, FERM domain C-lobe / Focal adhesion targeting region / FERM N-terminal domain / : / FAK1/PYK2, FERM domain C-lobe / FERM domain signature 2. / FERM central domain / FERM/acyl-CoA-binding protein superfamily / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / PH-like domain superfamily / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ubiquitin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Focal adhesion kinase 1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.004 Å
AuthorsMomin, A.A. / Shahul Hameed, U.F. / Arold, S.T.
Funding support Saudi Arabia, 1items
OrganizationGrant numberCountry
Other governmentKAUST - URF/1/2602-01-01 Saudi Arabia
CitationJournal: Sci Rep / Year: 2019
Title: Passenger sequences can promote interlaced dimers in a common variant of the maltose-binding protein.
Authors: Momin, A.A. / Hameed, U.F.S. / Arold, S.T.
History
DepositionNov 26, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 1.2Nov 22, 2023Group: 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: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
B: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
X: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
Y: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,6076
Polymers175,4144
Non-polymers1922
Water7,710428
1
A: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
B: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8033
Polymers87,7072
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22630 Å2
ΔGint-183 kcal/mol
Surface area31210 Å2
MethodPISA
2
X: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
Y: Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8033
Polymers87,7072
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22680 Å2
ΔGint-181 kcal/mol
Surface area31690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.910, 71.960, 83.390
Angle α, β, γ (deg.)97.840, 90.030, 106.550
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Maltose/maltodextrin-binding periplasmic protein,Focal adhesion kinase 1 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / FADK 1 / Focal adhesion ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / FADK 1 / Focal adhesion kinase-related nonkinase / FRNK / Protein phosphatase 1 regulatory subunit 71 / PPP1R71 / Protein-tyrosine kinase 2 / p125FAK / pp125FAK


Mass: 43853.605 Da / Num. of mol.: 4
Mutation: surface entropy reduction mutant,D83A,K84A,E173A,N174A,K240A,E360A,K363A,D364A
Source method: isolated from a genetically manipulated source
Details: residues 805-832 of the human focal adhesion kinase are C-terminally fused to the maltose-binding protein
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, PTK2, FAK, FAK1 / Plasmid: pJEx411c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0AEX9, UniProt: Q05397, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.35 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 10.5
Details: 2000mM Ammonium sulfate, 100mM CAPS/ Sodium hydroxide pH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→47.49 Å / Num. obs: 93102 / % possible obs: 95.33 % / Redundancy: 8.12 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.1033 / Rpim(I) all: 0.06574 / Rrim(I) all: 0.1229 / Χ2: 0.86 / Net I/σ(I): 8.07
Reflection shellResolution: 2.004→2.076 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.944 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 8178 / CC1/2: 0.6 / Rpim(I) all: 0.7233 / Χ2: 0.55 / % possible all: 84.49

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Processing

Software
NameVersionClassification
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BMY

5bmy


Resolution: 2.004→47.45 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 13.811 / SU ML: 0.175 / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.174
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 4656 5 %RANDOM
Rwork0.1999 ---
obs0.2015 88446 95.37 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso max: 129.9 Å2 / Biso mean: 50.329 Å2 / Biso min: 26.93 Å2
Baniso -1Baniso -2Baniso -3
1-3.35 Å20.29 Å20.3 Å2
2--0.34 Å20.58 Å2
3----3.97 Å2
Refinement stepCycle: final / Resolution: 2.004→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11300 0 10 428 11738
Biso mean--83.57 47.61 -
Num. residues----1472
LS refinement shellResolution: 2.004→2.056 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.368 288 -
Rwork0.3641 5468 -
obs--80.19 %
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)
17.08830.07381.27783.8231-0.37444.4010.07050.04510.66350.214-0.036-0.1806-0.60250.3337-0.03450.13-0.0822-0.02060.1334-0.08740.350724.841-12.31-25.912
24.05960.01350.39020.90450.05360.97780.06350.4248-0.0768-0.0995-0.00880.0672-0.037-0.0497-0.05470.0178-0.0074-0.01920.195-0.07710.31723.539-25.03-35.178
35.4431-0.2590.52550.52310.03760.4583-0.0394-0.02150.4842-0.1053-0.0456-0.1622-0.05370.14060.0850.0322-0.0137-0.01120.213-0.09460.48832.326-50.087-45.619
43.51220.04380.70972.25610.72043.25390.0305-0.2097-0.022-0.0355-0.04610.12030.2461-0.06520.01560.0228-0.0055-0.0010.1807-0.06530.384311.59-57.03-45.12
57.0781-0.82580.45360.6161-0.12710.3943-0.1088-0.23610.9216-0.0325-0.0396-0.2419-0.05080.04150.14840.019-0.0149-0.03710.2154-0.11610.494839.754-47.99-43.099
63.50050.10570.06750.71890.00511.04220.0860.26870.0871-0.0283-0.04140.0886-0.0707-0.1159-0.04460.0142-0.0042-0.0090.162-0.07120.34763.91-22.423-33.288
79.84631.3551-4.0542.45021.37248.9349-0.13130.91531.2969-0.69630.3372-0.2716-0.4361-0.0341-0.20590.32290.0089-0.05040.7790.10920.6545-4.691-14.75-54.661
85.3704-0.2765-1.4054.3221-0.54.7845-0.06080.0157-0.5503-0.2250.08520.18410.4178-0.35-0.02440.0607-0.05430.00080.0611-0.05530.446233.971-12.6186.927
93.86260.5390.18254.93772.12383.676-0.08020.33460.1595-0.32150.02150.1895-0.0103-0.18080.05860.0567-0.0341-0.02140.081-0.0470.3137.4872.740.114
106.09480.0297-0.43450.7171-0.11860.8031-0.12660.15370.2381-0.01920.039-0.0927-0.00840.09530.08760.0506-0.02670.04910.0494-0.05780.325756.9663.2455.342
116.707-0.17952.70962.6989-0.31294.3168-0.00650.0535-0.1477-0.1320.0239-0.47580.09420.3762-0.01740.02080.01580.08080.1559-0.03530.397976.872-1.7164.691
124.0947-2.35880.5491.4224-0.29270.51530.28910.8537-0.1854-0.217-0.42190.23290.19020.00980.13280.1572-0.0461-0.03890.3953-0.14450.752836.17514.266-12.019
135.66190.0565-0.72250.5512-0.20840.8164-0.1222-0.0948-0.28710.04120.10050.1963-0.0966-0.16870.02180.03780.0101-0.01830.1038-0.01880.421219.05231.9972.105
146.4364-0.0054-0.54252.3582-2.18732.6096-0.1467-0.6347-0.23010.1970.0098-0.0683-0.18680.23620.13690.0798-0.0187-0.02820.1874-0.03970.344849.95233.2397.538
153.4721-0.4475-0.96921.98862.72973.8466-0.0747-0.4303-0.50250.0484-0.0130.0830.0794-0.00510.08770.02230.03390.00940.12860.04770.498632.48626.4817.782
1610.8418-2.37841.98311.4341-1.09831.5826-0.22460.9001-0.0781-0.2480.1592-0.0917-0.0957-0.19230.06540.2141-0.0983-0.04370.4561-0.07010.502220.7929.519-19.09
175.0641-0.29810.00382.8856-0.7015.50140.0318-0.03130.27130.2499-0.0265-0.2864-0.43710.1942-0.00520.0975-0.0472-0.0110.0459-0.07020.394248.80241.5731.257
183.4891-0.56270.31240.74060.13760.7227-0.12250.0692-0.6102-0.05060.07930.14660.0315-0.03990.04320.0226-0.03-0.00140.0719-0.0330.520427.22325.807-1.01
193.01110.03050.49411.04160.00731.2023-0.04260.3011-0.0232-0.1811-0.022-0.16860.16530.23030.06450.06330.01340.07590.1064-0.08440.379163.572-1.0830.017
203.02190.0197-0.35841.0741-0.2241.2576-0.05610.2294-0.0951-0.19770.0231-0.0870.10620.05890.0330.0414-0.00570.0070.0689-0.09270.376649.616-1.2820.583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 64
2X-RAY DIFFRACTION2A65 - 173
3X-RAY DIFFRACTION3A174 - 371
4X-RAY DIFFRACTION4B5 - 98
5X-RAY DIFFRACTION5B99 - 172
6X-RAY DIFFRACTION6B173 - 353
7X-RAY DIFFRACTION7B354 - 373
8X-RAY DIFFRACTION8X5 - 64
9X-RAY DIFFRACTION9X65 - 98
10X-RAY DIFFRACTION10X99 - 132
11X-RAY DIFFRACTION11X133 - 154
12X-RAY DIFFRACTION12X155 - 201
13X-RAY DIFFRACTION13X202 - 268
14X-RAY DIFFRACTION14X269 - 297
15X-RAY DIFFRACTION15X298 - 334
16X-RAY DIFFRACTION16X335 - 371
17X-RAY DIFFRACTION17Y5 - 64
18X-RAY DIFFRACTION18Y65 - 174
19X-RAY DIFFRACTION19Y175 - 268
20X-RAY DIFFRACTION20Y269 - 374

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