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- PDB-5izs: De novo design of protein homo-oligomers with modular hydrogen bo... -

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Basic information

Entry
Database: PDB / ID: 5izs
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
ComponentsDesigned protein 5L6HC3_1Design
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsSankaran, B. / Zwart, P.H. / Pereira, J.H. / Baker, D. / Boyken, S. / Chen, Z. / Oberdorfer, G.
CitationJournal: Science / Year: 2016
Title: De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Authors: Boyken, S.E. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. / Gilmore, J.M. / Xu, C. / DiMaio, F. / Pereira, J.H. / Sankaran, B. / Seelig, G. / Zwart, P.H. / Baker, D.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 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

Downloads & links

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Assembly

Deposited unit
A: Designed protein 5L6HC3_1
B: Designed protein 5L6HC3_1
C: Designed protein 5L6HC3_1
D: Designed protein 5L6HC3_1
E: Designed protein 5L6HC3_1
F: Designed protein 5L6HC3_1


Theoretical massNumber of molelcules
Total (without water)67,8706
Polymers67,8706
Non-polymers00
Water2,252125
1
A: Designed protein 5L6HC3_1
B: Designed protein 5L6HC3_1
C: Designed protein 5L6HC3_1


Theoretical massNumber of molelcules
Total (without water)33,9353
Polymers33,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-46 kcal/mol
Surface area13180 Å2
MethodPISA
2
D: Designed protein 5L6HC3_1
E: Designed protein 5L6HC3_1
F: Designed protein 5L6HC3_1


Theoretical massNumber of molelcules
Total (without water)33,9353
Polymers33,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-53 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.670, 72.670, 88.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11C-118-

HOH

DetailsTrimer according to SEC-MALS and SAXS data

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Components

#1: Protein
Designed protein 5L6HC3_1 / Design


Mass: 11311.688 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Fluoride, 0.1 M MES pH 5.5 , 20 % PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→51.24 Å / Num. obs: 21259 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.148 / Net I/σ(I): 12
Reflection shellHighest resolution: 2.36 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→51.237 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1091 5.13 %
Rwork0.2453 --
obs0.2465 21249 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→51.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 0 125 4096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044005
X-RAY DIFFRACTIONf_angle_d0.6285345
X-RAY DIFFRACTIONf_dihedral_angle_d15.7731682
X-RAY DIFFRACTIONf_chiral_restr0.021629
X-RAY DIFFRACTIONf_plane_restr0.002702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3602-2.46760.31141350.26832554X-RAY DIFFRACTION100
2.4676-2.59770.30321400.25172531X-RAY DIFFRACTION100
2.5977-2.76050.30431430.25052483X-RAY DIFFRACTION99
2.7605-2.97360.29991350.2632541X-RAY DIFFRACTION99
2.9736-3.27280.30021190.24492566X-RAY DIFFRACTION100
3.2728-3.74620.23791540.22282479X-RAY DIFFRACTION99
3.7462-4.71930.20421270.21242543X-RAY DIFFRACTION99
4.7193-51.24950.30511380.29122461X-RAY DIFFRACTION96
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)
10.0779-0.02650.0318-0.0341-0.01430.0065-0.05670.02510.0590.07330.39060.29760.0379-0.1317-00.17460.10950.07980.17070.05610.15754.077821.6969-52.0694
20.01590.1556-0.00410.08450.04020.00440.0463-0.07920.1102-0.0434-0.078-0.0773-0.3037-0.0065-00.06260.078-0.01890.2349-0.04680.08974.0332.2614-51.4135
30.1172-0.019-0.04860.2154-0.03830.00810.056-0.0747-0.01640.01190.129-0.06650.1337-0.067300.09570.0292-0.05170.182-0.02550.164814.580915.6068-51.2362
40.0805-0.1985-0.0331-0.17060.03720.00990.0318-0.1596-0.1813-0.3383-0.00650.10360.3182-0.31810-0.023-0.0662-0.04730.25920.07840.21425.320110.3143-50.6115
50.05730.21-0.00640.02670.01130.00940.06710.00560.10070.11190.1076-0.1256-0.31460.014400.10240.0889-0.02660.1865-0.03450.13913.894628.0793-48.1624
6-0.1124-0.07550.0864-0.1214-0.05280.01980.304-0.1707-0.22680.2046-0.1985-0.21250.30620.2514-0-0.00160.08240.01630.1613-0.05810.171522.906523.0978-49.5644
7-0.1866-0.010.0548-0.2556-0.03210.01660.03720.07570.15410.6650.6928-0.70710.09580.2646-0-0.2541-0.180.20570.19190.02160.0519-6.463319.8146-11.4239
80.0315-0.10980.0219-0.0227-0.05330.0247-0.24360.11920.0913-0.017-0.3209-0.3241-0.30470.1123-00.054-0.1095-0.0480.1917-0.00240.0809-5.714830.1765-11.7574
90.00130.0105-0.0130.03940.00830.001-0.10450.15790.15860.40130.1607-0.1287-0.0716-0.07190-0.2313-0.13760.17240.30950.08340.0828-16.150926.673-12.6387
100.02140.20680.05610.1548-0.070.02270.2503-0.2698-0.2511-0.19340.3184-0.0162-0.23-0.321800.1846-0.01620.01610.26720.03160.1415-25.692322.2063-8.7518
110.06120.0808-0.0780.0349-0.01040.01440.11480.0696-0.0730.02720.01480.11970.0835-0.03700.1732-0.0152-0.03440.1782-0.00410.1408-17.775714.7855-12.9218
120.00850.13790.02190.02240.05590.0160.1989-0.1714-0.29890.0240.0984-0.15440.26780.1806-00.13490.0680.03840.0008-0.13510.1041-8.76549.0073-7.737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 82 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 44 )
4X-RAY DIFFRACTION4chain 'B' and (resid 45 through 82 )
5X-RAY DIFFRACTION5chain 'C' and (resid 4 through 41 )
6X-RAY DIFFRACTION6chain 'C' and (resid 42 through 85 )
7X-RAY DIFFRACTION7chain 'D' and (resid 3 through 44 )
8X-RAY DIFFRACTION8chain 'D' and (resid 45 through 84 )
9X-RAY DIFFRACTION9chain 'E' and (resid 4 through 41 )
10X-RAY DIFFRACTION10chain 'E' and (resid 42 through 84 )
11X-RAY DIFFRACTION11chain 'F' and (resid 3 through 41 )
12X-RAY DIFFRACTION12chain 'F' and (resid 42 through 82 )

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