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- PDB-7bat: A hexameric barrel state of a de novo coiled-coil assembly: CC-Ty... -

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Basic information

Entry
Database: PDB / ID: 7bat
TitleA hexameric barrel state of a de novo coiled-coil assembly: CC-Type2-(GgIaId)4
ComponentsCC-Type2-(GgIaId)4
KeywordsDE NOVO PROTEIN / alpha / helical / barrel / hexamer
Function / homologyN-PROPANOL
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.77 Å
AuthorsMartin, F.J.O. / Dawson, W.M. / Shelley, K. / Brady, R.L. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
European Research Council (ERC)340764 United Kingdom
Engineering and Physical Sciences Research CouncilEP/G036764 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00661X/1 United Kingdom
CitationJournal: Chem Sci / Year: 2021
Title: Coiled coils 9-to-5: rational de novo design of alpha-helical barrels with tunable oligomeric states.
Authors: Dawson, W.M. / Martin, F.J.O. / Rhys, G.G. / Shelley, K.L. / Brady, R.L. / Woolfson, D.N.
History
DepositionDec 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 17, 2021Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / database_2 / diffrn_source / pdbx_database_proc / struct
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._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_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct.pdbx_center_of_mass_x / _struct.pdbx_center_of_mass_y / _struct.pdbx_center_of_mass_z

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CC-Type2-(GgIaId)4
B: CC-Type2-(GgIaId)4
C: CC-Type2-(GgIaId)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,7176
Polymers9,5363
Non-polymers1803
Water37821
1
A: CC-Type2-(GgIaId)4
B: CC-Type2-(GgIaId)4
C: CC-Type2-(GgIaId)4
hetero molecules

A: CC-Type2-(GgIaId)4
B: CC-Type2-(GgIaId)4
C: CC-Type2-(GgIaId)4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,43312
Polymers19,0736
Non-polymers3616
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area9710 Å2
ΔGint-75 kcal/mol
Surface area8240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.887, 42.736, 126.197
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-101-

POL

21A-101-

POL

31C-101-

POL

41A-206-

HOH

51A-207-

HOH

61A-208-

HOH

71B-201-

HOH

81C-201-

HOH

91C-203-

HOH

101C-204-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 28
2010B1 - 28
1020A1 - 27
2020C1 - 27
1030B1 - 27
2030C1 - 27

NCS ensembles :
ID
1
2
3

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Components

#1: Protein/peptide CC-Type2-(GgIaId)4


Mass: 3178.767 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-POL / N-PROPANOL / 1-PROPONOL / Propan-1-ol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.82 Å3/Da / Density % sol: 56.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.5 mM peptide, 50 mM MES, 5 % w/v PEG 5000 MME, 6 % v/v 1-propanol.
Temp details: 20 degC incubator

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: DIAMOND / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→40.48 Å / Num. obs: 10914 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.012 / Rrim(I) all: 0.041 / Net I/σ(I): 21.6
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
1.77-1.8111.93.32471165960.3870.993.4730.6100
9.03-40.489.70.02710211050.9980.0110.0362.399

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
DIALSdata reduction
Arcimboldolitephasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.77→40.48 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.943 / SU B: 6.617 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1321 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 514 4.7 %RANDOM
Rwork0.2584 ---
obs0.2585 10397 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 94.32 Å2 / Biso mean: 46.427 Å2 / Biso min: 31.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.29 Å20 Å2-0 Å2
2--0.72 Å20 Å2
3----2.01 Å2
Refinement stepCycle: final / Resolution: 1.77→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 12 21 634
Biso mean--51.88 67.6 -
Num. residues----89
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.013613
X-RAY DIFFRACTIONr_bond_other_d0.0010.018641
X-RAY DIFFRACTIONr_angle_refined_deg1.1191.624813
X-RAY DIFFRACTIONr_angle_other_deg1.2461.5871462
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.55584
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.6192516
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25115107
X-RAY DIFFRACTIONr_chiral_restr0.0470.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02682
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02110
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A7190.08
12B7190.08
21A6990.07
22C6990.07
31B6760.08
32C6760.08
LS refinement shellResolution: 1.77→1.816 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 37 -
Rwork0.439 750 -
all-787 -
obs--100 %
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)
10.97910.03760.04071.7047-1.08376.70370.01270.05690.01540.0155-0.0117-0.0754-0.04220.1952-0.0010.00380.01140.00750.05670.00410.109828.033420.789522.6164
22.0768-0.3812.19111.6308-0.91247.1649-0.03830.05180.04430.03780.0135-0.0472-0.24640.15540.02480.0179-0.0208-0.0010.0340.00560.09425.035428.116123.2994
31.36320.0943-0.53351.4787-0.69336.05560.0250.0348-0.0528-0.07180.0568-0.05360.19740.1819-0.08190.040.01790.00680.01820.00540.105224.488414.38920.8342
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 29
2X-RAY DIFFRACTION2B1 - 30
3X-RAY DIFFRACTION3C0 - 28

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