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- PDB-5j7c: A picomolar affinity FN3 domain in complex with hen egg-white lysozyme -

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Basic information

Entry
Database: PDB / ID: 5j7c
TitleA picomolar affinity FN3 domain in complex with hen egg-white lysozyme
Components
  • FNfn10-anti-lysozyme (DE0.4.1)
  • Lysozyme C
Keywordsprotein binding/hydrolase / Yeast surface display / high affinity / fibronectin type III / FN3 / protein binding-hydrolase complex
Function / homology
Function and homology information


negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking ...negative regulation of monocyte activation / calcium-independent cell-matrix adhesion / negative regulation of transforming growth factor beta production / Fibronectin matrix formation / Extracellular matrix organization / positive regulation of substrate-dependent cell migration, cell attachment to substrate / neural crest cell migration involved in autonomic nervous system development / peptidase activator activity / fibrinogen complex / peptide cross-linking / integrin activation / ALK mutants bind TKIs / cell-substrate junction assembly / biological process involved in interaction with symbiont / Molecules associated with elastic fibres / proteoglycan binding / extracellular matrix structural constituent / MET activates PTK2 signaling / Syndecan interactions / p130Cas linkage to MAPK signaling for integrins / endodermal cell differentiation / GRB2:SOS provides linkage to MAPK signaling for Integrins / Non-integrin membrane-ECM interactions / Signaling by ALK fusions and activated point mutants / basement membrane / endoplasmic reticulum-Golgi intermediate compartment / ECM proteoglycans / positive regulation of axon extension / Integrin cell surface interactions / Nuclear events stimulated by ALK signaling in cancer / collagen binding / extracellular matrix / Degradation of the extracellular matrix / cell-matrix adhesion / Integrin signaling / substrate adhesion-dependent cell spreading / regulation of ERK1 and ERK2 cascade / platelet alpha granule lumen / Antimicrobial peptides / Neutrophil degranulation / integrin-mediated signaling pathway / beta-N-acetylglucosaminidase activity / Post-translational protein phosphorylation / acute-phase response / Cell surface interactions at the vascular wall / regulation of protein phosphorylation / Signaling by high-kinase activity BRAF mutants / wound healing / MAP2K and MAPK activation / response to wounding / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / GPER1 signaling / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / cell wall macromolecule catabolic process / integrin binding / Platelet degranulation / lysozyme / heparin binding / lysozyme activity / nervous system development / heart development / regulation of cell shape / collagen-containing extracellular matrix / angiogenesis / blood microparticle / Interleukin-4 and Interleukin-13 signaling / killing of cells of another organism / protease binding / defense response to Gram-negative bacterium / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / defense response to Gram-positive bacterium / defense response to bacterium / apical plasma membrane / endoplasmic reticulum lumen / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. ...Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / Fibronectin type II domain / Fibronectin type II domain superfamily / Fibronectin type II domain / Fibronectin type-II collagen-binding domain signature. / Fibronectin type-II collagen-binding domain profile. / Fibronectin type 2 domain / Kringle-like fold / EGF-like domain signature 1. / Lysozyme - #10 / Fibronectin type III domain / Fibronectin type 3 domain / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Fibronectin
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.535 Å
AuthorsPorebski, B.T. / Drinkwater, N. / McGowan, S. / Buckle, A.M.
CitationJournal: Protein Eng.Des.Sel. / Year: 2016
Title: Circumventing the stability-function trade-off in an engineered FN3 domain.
Authors: Porebski, B.T. / Conroy, P.J. / Drinkwater, N. / Schofield, P. / Vazquez-Lombardi, R. / Hunter, M.R. / Hoke, D.E. / Christ, D. / McGowan, S. / Buckle, A.M.
History
DepositionApr 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
C: FNfn10-anti-lysozyme (DE0.4.1)
D: FNfn10-anti-lysozyme (DE0.4.1)


Theoretical massNumber of molelcules
Total (without water)51,2564
Polymers51,2564
Non-polymers00
Water93752
1
A: Lysozyme C
C: FNfn10-anti-lysozyme (DE0.4.1)


Theoretical massNumber of molelcules
Total (without water)25,6282
Polymers25,6282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area10620 Å2
MethodPISA
2
B: Lysozyme C
D: FNfn10-anti-lysozyme (DE0.4.1)


Theoretical massNumber of molelcules
Total (without water)25,6282
Polymers25,6282
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7 kcal/mol
Surface area10850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.858, 87.725, 100.895
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Protein FNfn10-anti-lysozyme (DE0.4.1)


Mass: 11296.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P02751*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.37 Å3/Da / Density % sol: 48.06 % / Description: Long thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 / Details: 10% PEG 6000, 0.1 M Bicine, pH 8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.535→46.51 Å / Num. obs: 16719 / % possible obs: 99 % / Redundancy: 6.7 % / CC1/2: 0.993 / Rmerge(I) obs: 0.244 / Net I/σ(I): 8.9
Reflection shellResolution: 2.535→2.626 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.264 / Mean I/σ(I) obs: 2.13 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155:000)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FNF, 4Z98

1fnf

4z98


Resolution: 2.535→46.51 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.51
RfactorNum. reflection% reflectionSelection details
Rfree0.2498 830 4.98 %Random selection
Rwork0.2176 ---
obs0.2192 16666 99.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 37.52 Å2
Refinement stepCycle: LAST / Resolution: 2.535→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 0 52 3482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023521
X-RAY DIFFRACTIONf_angle_d0.5624805
X-RAY DIFFRACTIONf_dihedral_angle_d13.2972043
X-RAY DIFFRACTIONf_chiral_restr0.046523
X-RAY DIFFRACTIONf_plane_restr0.005618
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5351-2.6940.30291140.29272530X-RAY DIFFRACTION97
2.694-2.90190.26761470.27942610X-RAY DIFFRACTION100
2.9019-3.19390.33061310.26692629X-RAY DIFFRACTION100
3.1939-3.65590.25661620.21712619X-RAY DIFFRACTION100
3.6559-4.60540.21141310.18082665X-RAY DIFFRACTION100
4.6054-46.51990.21341450.17892783X-RAY DIFFRACTION100
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)
14.19032.26721.45723.5836-0.16350.9204-0.1481.1921-0.7569-0.51750.37180.08420.33930.5674-0.14590.13350.01190.08870.5876-0.22840.5746-7.9804-13.23892.9375
24.611-0.01130.57276.74620.0653.98180.01131.1476-1.0695-0.43820.2111-0.06820.43330.2935-0.23760.21890.0193-0.0220.4412-0.18410.4787-16.9263-14.31363.627
33.8899-1.8126-0.25472.4453-1.36575.3419-0.0497-0.2928-0.17390.02050.08690.1121-0.23640.0923-0.03810.19540.0234-0.00610.2003-0.02990.2855-24.3648-2.971214.1071
49.0058-0.1422-0.99854.1723.10242.895-0.2728-1.3512-1.13630.9416-0.051-0.20460.9905-0.41580.47460.38050.04120.15670.3840.05370.2879-26.2807-8.396621.7051
51.56171.2704-1.76613.7449-0.33992.365-0.3875-0.2798-0.96680.6670.3625-0.0412-0.17110.05520.03390.1680.0782-0.07210.3330.04320.4967-15.7708-11.768714.494
66.7896-0.51962.9930.051-0.09083.6829-0.2829-0.2677-1.19410.1103-0.07460.42670.548-0.71230.10380.1695-0.05610.02220.5007-0.15630.8553-27.6116-16.46197.4697
76.6304-4.9091-2.81984.96811.84272.07220.72351.8847-1.0423-0.7814-0.422-0.0846-0.0243-0.1615-0.28680.37130.0311-0.01890.7778-0.30080.5605-19.3299-14.8594-4.0251
82.28110.32120.71129.26213.65767.25770.2507-0.10530.3548-0.3941-0.34020.373-0.4441-1.00160.28310.26080.1292-0.05310.4654-0.1660.2669-81.948727.585812.985
95.266-1.0991-3.90954.5898-2.38635.30640.0914-0.11410.55740.4754-0.1465-0.4833-0.8468-0.47540.06680.41760.0894-0.03590.3164-0.10930.3309-71.333834.921319.4867
100.4933-0.17470.0110.3972-0.60281.18750.01080.5770.163-0.5847-0.48380.213-0.12830.48370.44120.33460.1781-0.12850.4799-0.0740.2928-71.749327.42610.0571
115.99440.10991.89491.31640.12481.31110.51340.6387-1.19770.0823-0.56540.48330.13050.09740.01350.21350.0543-0.06180.3669-0.10.2974-69.586713.345212.3934
123.3597-3.89121.2046.2619-1.79427.36170.40970.07320.2258-0.9356-0.24840.0895-0.19170.1875-0.11330.2550.0450.00340.2968-0.02010.304-69.753416.614916.0327
131.9956-2.91860.01418.2196-2.62561.7290.199-0.0769-0.0178-0.12190.05450.76680.1165-0.0952-0.27880.1740.008-0.02480.3985-0.02670.2981-63.723213.101622.5471
146.6082-4.2072-3.53494.66995.1576.1881-0.4398-0.60470.18340.39220.50170.22410.71950.7437-0.08090.35740.0378-0.06730.27450.02990.2618-63.525214.696627.2445
150.9085-1.21590.22382.96930.45073.4244-0.1692-0.0677-0.36590.00210.22920.1265-0.1146-0.0194-0.10910.21780.0561-0.00820.3529-0.05940.3119-73.517321.411422.4844
169.54013.32220.19055.05434.28634.55211.0746-1.3757-0.48810.16080.086-0.5842-0.01450.2026-1.14780.34840.018-0.04410.42020.02370.3282-61.707727.909617.6915
174.6106-0.48111.18136.1833-2.8828.67221.07610.91160.6644-1.04080.1564-0.0918-0.4325-0.2426-1.06530.4250.1730.11650.4281-0.01790.4016-63.868629.10396.9682
187.0381-2.4406-5.02616.83142.21093.62441.39860.20490.5996-1.5392-0.74120.5931-0.6123-0.0266-0.4350.71810.2764-0.00960.5941-0.03670.2634-77.764935.42956.0173
198.5663-3.41455.48026.657-4.18674.2659-0.88333.533-0.47260.02491.22890.5371-0.46970.7715-0.24090.2577-0.00420.0020.7267-0.01590.3619-53.2936-6.8974-2.4337
204.22470.9696-2.88061.5446-0.79553.411-0.26660.3775-0.58960.1165-0.0931-0.4528-0.1713-0.04080.30080.17480.0278-0.07970.26180.06610.3587-45.6755-7.20619.9115
213.193-1.2191-3.06563.6167-0.85884.31470.072-0.6948-0.62860.3031-0.12640.3659-0.06080.05360.0860.19510.07140.01840.3167-0.08540.2426-45.93231.011319.8308
224.96262.6681.21858.82992.38668.0091-0.30470.1474-1.2386-0.37010.6321-0.05520.36960.2262-0.34070.2620.04640.040.20930.04570.3454-40.7154-12.272710.8668
234.51161.2561-6.58862.0311-1.67842.11070.4717-0.05460.1224-0.0566-0.17130.1396-0.7823-0.128-0.17880.23980.0138-0.05260.31570.03940.282-50.3533-2.671615.944
244.4889-2.3972-1.50642.07260.08783.1918-0.94382.06040.9239-0.02070.47820.12390.1861-0.30240.37950.2656-0.1187-0.04060.53240.1610.4584-32.59961.35481.8663
257.56781.6148-4.66350.363-0.96282.99840.15090.50480.4586-0.10170.05830.6842-0.20780.2056-0.2275-0.71020.21740.31060.36990.09590.4998-55-2.062511.0258
264.3408-2.58252.44357.93521.29987.2107-0.2261-1.5851-0.89630.73670.1760.540.0135-1.19990.0760.3064-0.0817-0.05370.77980.07070.3902-63.2774-10.97422.6984
277.1961-5.26641.31314.23060.60996.7565-0.3034-0.29480.55730.70620.0982-0.82710.42151.10370.27810.29720.12970.00480.5496-0.06860.3265-34.947326.18664.8146
285.78432.50024.59771.62.34457.6019-0.16620.56090.12450.02110.1251-0.06290.34150.7449-0.02890.15430.04770.05730.2617-0.01450.2672-37.913221.19119.624
297.0465-4.12062.71875.1989-1.84722.1034-0.03760.1782-0.12590.29930.12220.0767-0.0967-0.0253-0.04180.21040.00370.0630.25-0.11050.2007-49.594116.764913.0802
307.4927-3.8668-0.07652.1796-0.36430.988-0.3314-0.6862-0.03640.18210.1360.42190.3834-0.535-0.0156-0.11120.13910.0110.2501-0.09630.5238-43.83687.119421.2954
312.4433.16460.52627.3663-4.09547.1128-0.09570.47770.05470.80280.0497-0.64040.1328-0.74660.06370.31790.0865-0.04390.3818-0.10150.2938-53.061824.120117.3882
327.3997-3.93216.99745.5831-6.80879.3728-0.0345-0.2136-0.25150.42940.16820.245-0.7964-0.3663-0.05470.23530.05230.01190.3791-0.07490.2509-37.944616.767524.5851
335.47641.71733.14935.2971-3.18625.4348-0.05810.6214-0.66360.1366-0.6185-0.74680.38950.38320.02770.17740.0473-0.0040.3105-0.1950.0049-42.821212.150115.7462
346.28330.43012.00091.6227-0.02910.6677-0.35160.11340.42820.10920.14830.29060.20860.030.20870.2070.0823-0.0280.3356-0.06270.2319-57.409114.55945.3108
357.84350.14245.86860.00140.11464.3992-0.12430.0573-0.5342-0.14060.4257-0.3083-0.70980.5802-0.34390.29630.1366-0.00920.5097-0.17690.265-34.775213.706714.8476
360.67180.01871.08630.29890.37112.9427-0.24590.0116-0.42840.04340.1179-0.04090.09270.14060.00670.87010.40350.24450.523-0.21020.2857-27.357416.099127.8079
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:14 )A1 - 14
2X-RAY DIFFRACTION2( CHAIN A AND RESID 15:42 )A15 - 42
3X-RAY DIFFRACTION3( CHAIN A AND RESID 43:68 )A43 - 68
4X-RAY DIFFRACTION4( CHAIN A AND RESID 69:78 )A69 - 78
5X-RAY DIFFRACTION5( CHAIN A AND RESID 79:99 )A79 - 99
6X-RAY DIFFRACTION6( CHAIN A AND RESID 100:108 )A100 - 108
7X-RAY DIFFRACTION7( CHAIN A AND RESID 109:129 )A109 - 129
8X-RAY DIFFRACTION8( CHAIN B AND RESID 1:14 )B1 - 14
9X-RAY DIFFRACTION9( CHAIN B AND RESID 15:24 )B15 - 24
10X-RAY DIFFRACTION10( CHAIN B AND RESID 25:36 )B25 - 36
11X-RAY DIFFRACTION11( CHAIN B AND RESID 37:50 )B37 - 50
12X-RAY DIFFRACTION12( CHAIN B AND RESID 51:58 )B51 - 58
13X-RAY DIFFRACTION13( CHAIN B AND RESID 59:68 )B59 - 68
14X-RAY DIFFRACTION14( CHAIN B AND RESID 69:78 )B69 - 78
15X-RAY DIFFRACTION15( CHAIN B AND RESID 79:100 )B79 - 100
16X-RAY DIFFRACTION16( CHAIN B AND RESID 101:108 )B101 - 108
17X-RAY DIFFRACTION17( CHAIN B AND RESID 109:119 )B109 - 119
18X-RAY DIFFRACTION18( CHAIN B AND RESID 120:128 )B120 - 128
19X-RAY DIFFRACTION19( CHAIN C AND RESID 4:7 )C4 - 7
20X-RAY DIFFRACTION20( CHAIN C AND RESID 8:37 )C8 - 37
21X-RAY DIFFRACTION21( CHAIN C AND RESID 38:47 )C38 - 47
22X-RAY DIFFRACTION22( CHAIN C AND RESID 48:60 )C48 - 60
23X-RAY DIFFRACTION23( CHAIN C AND RESID 61:75 )C61 - 75
24X-RAY DIFFRACTION24( CHAIN C AND RESID 76:87 )C76 - 87
25X-RAY DIFFRACTION25( CHAIN C AND RESID 88:93 )C88 - 93
26X-RAY DIFFRACTION26( CHAIN C AND RESID 94:99 )C94 - 99
27X-RAY DIFFRACTION27( CHAIN D AND RESID 2:7 )D2 - 7
28X-RAY DIFFRACTION28( CHAIN D AND RESID 8:22 )D8 - 22
29X-RAY DIFFRACTION29( CHAIN D AND RESID 23:37 )D23 - 37
30X-RAY DIFFRACTION30( CHAIN D AND RESID 38:47 )D38 - 47
31X-RAY DIFFRACTION31( CHAIN D AND RESID 48:55 )D48 - 55
32X-RAY DIFFRACTION32( CHAIN D AND RESID 56:66 )D56 - 66
33X-RAY DIFFRACTION33( CHAIN D AND RESID 67:75 )D67 - 75
34X-RAY DIFFRACTION34( CHAIN D AND RESID 76:87 )D76 - 87
35X-RAY DIFFRACTION35( CHAIN D AND RESID 88:93 )D88 - 93
36X-RAY DIFFRACTION36( CHAIN D AND RESID 94:98 )D94 - 98

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