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- PDB-5l2h: Crystal Structure of W26A mutant of anti-EGFR Centyrin P54AR4-83v2 -

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Basic information

Entry
Database: PDB / ID: 5l2h
TitleCrystal Structure of W26A mutant of anti-EGFR Centyrin P54AR4-83v2
ComponentsCentyrin
KeywordsDE NOVO PROTEIN / scaffold protein / fibronectin type III / beta sandwich
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8013 Å
AuthorsCardoso, R.M.F. / Goldberg, S.D. / O Neil, K.T. / Gilliland, G.L.
CitationJournal: Protein Eng. Des. Sel. / Year: 2016
Title: Engineering a targeted delivery platform using Centyrins.
Authors: Goldberg, S.D. / Cardoso, R.M. / Lin, T. / Spinka-Doms, T. / Klein, D. / Jacobs, S.A. / Dudkin, V. / Gilliland, G. / O'Neil, K.T.
History
DepositionAug 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centyrin
B: Centyrin
C: Centyrin
D: Centyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0676
Polymers45,8834
Non-polymers1842
Water6,467359
1
A: Centyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,4711
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Centyrin


Theoretical massNumber of molelcules
Total (without water)11,4711
Polymers11,4711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Centyrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5632
Polymers11,4711
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Centyrin


Theoretical massNumber of molelcules
Total (without water)11,4711
Polymers11,4711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.350, 61.709, 59.515
Angle α, β, γ (deg.)90.000, 100.410, 90.000
Int Tables number4
Space group name H-MP1211
DetailsMonomer confirmed by gel filtration

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Components

#1: Protein
Centyrin


Mass: 11470.756 Da / Num. of mol.: 4 / Fragment: Fibronectin type III domain variant / Mutation: W26A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pJexpress401 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 GOLD cells
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.34 Å3/Da / Density % sol: 47.35 % / Mosaicity: 0.37 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 25% PEG 3 kDa, 1 M sodium acetate, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 38977 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 23.65 Å2 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.025 / Rrim(I) all: 0.046 / Χ2: 0.931 / Net I/av σ(I): 25.4 / Net I/σ(I): 12.1 / Num. measured all: 127861
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3 % / Rmerge(I) obs: 0.186 / CC1/2: 0.953 / % possible all: 99.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data reduction
PHASER2.1.4phasing
PHENIX1.10_2155refinement
Cootmodel building
PDB_EXTRACT3.2data extraction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8013→32.381 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / Phase error: 21.54
RfactorNum. reflection% reflection
Rfree0.1993 1955 5.02 %
Rwork0.1644 --
obs0.1663 38952 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 82.91 Å2 / Biso mean: 33.4226 Å2 / Biso min: 13.1 Å2
Refinement stepCycle: final / Resolution: 1.8013→32.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 12 359 3296
Biso mean--50.15 43.58 -
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093053
X-RAY DIFFRACTIONf_angle_d1.0074187
X-RAY DIFFRACTIONf_chiral_restr0.073491
X-RAY DIFFRACTIONf_plane_restr0.007534
X-RAY DIFFRACTIONf_dihedral_angle_d15.4391821
LS refinement shellResolution: 1.8013→1.8463 Å
RfactorNum. reflection% reflection
Rfree0.2346 136 -
Rwork0.2038 2561 -
obs--98 %
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)
19.1901-0.0206-6.21952.5603-1.30882.0712-0.1848-0.3892-0.53190.1308-0.1763-0.05760.6721-0.62640.3140.1828-0.07010.00760.1860.02550.17874.0843-13.136552.7006
22.201-1.223-5.48126.76482.15777.42370.18770.82110.9734-0.38750.1265-0.3734-0.06860.7349-0.31620.15190.0302-0.00030.38910.03270.21216.7175-8.97337.8905
35.6341-3.6448-5.3234.34023.86442.1041-0.16250.311-0.0632-0.0405-0.1280.3073-0.4329-1.1860.27920.21420.0340.0310.26650.01750.25262.9642-5.284252.5669
42.5611-5.9017-6.43687.76654.855810.0978-0.6007-0.60140.07870.64190.5997-0.4820.6430.9527-0.15890.16390.0614-0.02750.2006-0.03420.2418.0544-10.159251.6507
55.4216-3.44040.56527.23441.99081.14790.13080.0405-1.62250.58120.2039-0.51021.8231.1563-0.36620.61740.2475-0.09770.55240.02280.690927.0379-18.316151.608
61.9691.90373.25611.96690.5134.9657-0.2933-0.28850.37490.25670.0776-0.54120.0540.54890.05720.18060.02970.02530.2110.01640.234417.4092-3.897852.8044
72.1779-5.5251-5.43746.48523.2227.5399-0.02630.2970.89950.19080.1869-0.581-0.30190.1314-0.28330.1701-0.0161-0.01870.19390.00110.228613.1506-2.585145.7478
86.4604-4.0471-3.63548.33573.75627.8964-0.47950.3353-0.1466-0.24040.5508-1.45770.61091.2381-0.22040.2640.13880.05380.5953-0.10410.393927.144-13.189339.9511
97.5803-4.0506-5.87624.5013.09313.8197-0.0721-0.1269-0.28110.07590.12340.03840.1270.4575-0.17170.20230.0964-0.01320.17320.00540.191112.4965-9.984956.0952
106.7263-2.8804-4.88834.17293.31053.0446-0.1126-0.0396-0.00640.17980.2393-0.14420.38230.4549-0.17810.19980.0549-0.03310.14880.02160.193313.5274-11.847653.5744
117.8363-0.2032-9.21476.17710.2212.17130.47530.20640.6706-0.31860.0316-0.4665-0.65410.2203-0.49910.2508-0.0189-0.0140.2993-0.03690.351612.3421-6.788924.2577
128.69296.7631-5.88722.3236-6.85359.25260.3199-0.15740.25740.84120.11890.7208-0.3171-0.7624-0.61510.29750.00460.05020.31790.00760.2885-2.1282-15.06639.0354
135.62870.1408-0.44946.484-2.34997.14560.05610.12610.4463-0.0335-0.1699-0.0204-0.4015-0.02660.09990.196-0.0209-0.03580.1686-0.0320.18674.8823-10.679725.0321
142.63262.5164-0.84343.59020.36114.59110.07270.0728-0.25960.0424-0.1359-0.02810.5324-0.2352-0.07870.2414-0.016-0.04030.2319-0.05160.23751.6386-18.579429.5177
154.07861.2947-4.90973.8537-4.49539.23950.32890.25090.36680.16750.04210.0168-0.3333-0.0056-0.28970.1638-0.001-0.01960.1357-0.02960.19788.4253-13.791322.1273
163.53480.3707-0.65232.5692-1.68449.05330.01030.23560.0785-0.0633-0.0417-0.09640.32080.3583-0.03670.14340.02020.00760.0787-0.03410.17348.8226-14.969325.8985
172.0585-0.9418-1.55092.9049-0.66337.22520.1287-1.0920.7289-0.153-0.09550.2954-0.351-0.5094-0.0210.17310.051-0.00590.1848-0.07960.2168-2.345411.47944.9552
188.83731.24081.94989.63041.26112.0539-0.4880.55940.0537-0.39190.3761-0.69640.88021.51280.17090.22340.0290.03310.42250.04750.201216.28297.935633.7501
197.06253.4713-2.1421.8832-1.97075.10230.0999-0.7934-0.44450.1857-0.1169-0.04820.05150.1843-0.01520.20820.01210.0110.19370.03570.19491.00384.280443.886
202.66385.0327-6.69948.4159-8.41092.83130.04950.86820.6813-0.34660.57920.7949-0.0996-0.3529-0.53880.2988-0.07-0.00720.30110.10910.25371.2098.511531.3803
211.67032.78430.39926.0951-1.54252.7359-1.03021.91612.2764-1.51770.6130.6509-0.85160.70710.50.6263-0.0503-0.11310.60340.27720.69262.718416.503122.426
224.50216.3985-5.96541.92431.77291.91030.10080.5208-0.2-0.54860.0670.09720.5437-0.09440.13740.26980.01120.01770.20230.02970.228-0.04762.258431.8265
232.16149.2805-1.55616.7601-1.64738.4776-0.0335-0.0749-0.3527-0.27110.0241-0.19730.67670.49620.04950.20550.06340.02650.20590.03710.25475.6970.736638.4364
242.1013.7558-5.39087.48781.7545.5102-0.08071.23340.3902-0.85790.463-0.7286-0.01561.1231-0.17520.3223-0.10.02830.53270.12280.271613.833110.17525.0666
256.01461.9621-3.493.1777-2.10975.52410.0031-0.10810.2382-0.1147-0.07250.1932-0.18390.2951-0.00980.2105-0.00350.0020.09530.04960.2045-3.95388.331536.1332
262.14121.9501-9.23322.0915-8.79546.4043-0.44930.763-0.4058-1.4430.02950.44320.6462-0.4040.29790.36340.0042-0.05560.3229-0.03540.3467-14.80273.690136.1783
276.6153.1382-6.0285.0792-1.23558.60160.1668-0.3350.85680.04610.1578-0.188-0.51720.8732-0.27620.2233-0.0563-0.01980.21650.06850.24916.962914.351235.0779
283.2054-2.1036-4.95185.09260.94828.7606-0.5905-0.8023-0.43750.12460.32710.35640.65470.3350.34080.1944-0.0336-0.08420.1894-0.07180.18317.99279.413148.0365
295.75130.0411.18447.8871-0.7475.64260.1383-0.2348-0.14060.0902-0.1487-0.11420.12910.00180.02450.1793-0.0355-0.02820.2162-0.02020.172224.013111.480150.5204
306.9772-2.4112-2.34752.47250.51862.8351-0.2792-0.0994-0.05010.10070.00730.15920.08440.14230.24590.2058-0.0299-0.03630.1201-0.02020.160423.668414.990947.9001
312.5209-2.22451.36313.1012-0.24924.1059-0.21810.33010.3660.01720.015-0.03650.03710.44730.21810.1882-0.02730.00280.1348-0.01870.156425.533313.342345.4291
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 8 )A1 - 8
2X-RAY DIFFRACTION2chain 'A' and (resid 9 through 21 )A9 - 21
3X-RAY DIFFRACTION3chain 'A' and (resid 22 through 30 )A22 - 30
4X-RAY DIFFRACTION4chain 'A' and (resid 31 through 38 )A31 - 38
5X-RAY DIFFRACTION5chain 'A' and (resid 39 through 45 )A39 - 45
6X-RAY DIFFRACTION6chain 'A' and (resid 46 through 51 )A46 - 51
7X-RAY DIFFRACTION7chain 'A' and (resid 52 through 60 )A52 - 60
8X-RAY DIFFRACTION8chain 'A' and (resid 61 through 66 )A61 - 66
9X-RAY DIFFRACTION9chain 'A' and (resid 67 through 79 )A67 - 79
10X-RAY DIFFRACTION10chain 'A' and (resid 80 through 97 )A80 - 97
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 8 )B1 - 8
12X-RAY DIFFRACTION12chain 'B' and (resid 9 through 17 )B9 - 17
13X-RAY DIFFRACTION13chain 'B' and (resid 18 through 38 )B18 - 38
14X-RAY DIFFRACTION14chain 'B' and (resid 39 through 66 )B39 - 66
15X-RAY DIFFRACTION15chain 'B' and (resid 67 through 79 )B67 - 79
16X-RAY DIFFRACTION16chain 'B' and (resid 80 through 98 )B80 - 98
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 8 )C1 - 8
18X-RAY DIFFRACTION18chain 'C' and (resid 9 through 17 )C9 - 17
19X-RAY DIFFRACTION19chain 'C' and (resid 18 through 30 )C18 - 30
20X-RAY DIFFRACTION20chain 'C' and (resid 31 through 38 )C31 - 38
21X-RAY DIFFRACTION21chain 'C' and (resid 39 through 45 )C39 - 45
22X-RAY DIFFRACTION22chain 'C' and (resid 46 through 51 )C46 - 51
23X-RAY DIFFRACTION23chain 'C' and (resid 52 through 59 )C52 - 59
24X-RAY DIFFRACTION24chain 'C' and (resid 60 through 66 )C60 - 66
25X-RAY DIFFRACTION25chain 'C' and (resid 67 through 79 )C67 - 79
26X-RAY DIFFRACTION26chain 'C' and (resid 80 through 85 )C80 - 85
27X-RAY DIFFRACTION27chain 'C' and (resid 86 through 97 )C86 - 97
28X-RAY DIFFRACTION28chain 'D' and (resid 1 through 17 )D1 - 17
29X-RAY DIFFRACTION29chain 'D' and (resid 18 through 59 )D18 - 59
30X-RAY DIFFRACTION30chain 'D' and (resid 60 through 79 )D60 - 79
31X-RAY DIFFRACTION31chain 'D' and (resid 80 through 98 )D80 - 98

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