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- PDB-8bct: X-ray crystal structure of a de novo selected helix-loop-helix he... -

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Basic information

Entry
Database: PDB / ID: 8bct
TitleX-ray crystal structure of a de novo selected helix-loop-helix heterodimer in a syn arrangement, 26alpha/26beta
Components
  • 26alpha
  • 26beta
KeywordsDE NOVO PROTEIN / coiled coil / 4-helix bundle / in-cell library screening / protein-protein interactions
Function / homologyACETATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsNaudin, E.A. / Mylemans, B. / Smith, A.J. / Savery, N.J. / Woolfson, D.N.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S002820/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V006231/1 United Kingdom
Max Planck Bristol Centre for Minimal Biology - University of Bristol United Kingdom
CitationJournal: Acs Synth Biol / Year: 2023
Title: Design and Selection of Heterodimerizing Helical Hairpins for Synthetic Biology.
Authors: Smith, A.J. / Naudin, E.A. / Edgell, C.L. / Baker, E.G. / Mylemans, B. / FitzPatrick, L. / Herman, A. / Rice, H.M. / Andrews, D.M. / Tigue, N. / Woolfson, D.N. / Savery, N.J.
History
DepositionOct 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 26alpha
G: 26beta
B: 26alpha
E: 26beta
H: 26alpha
A: 26beta
C: 26beta
F: 26alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,53522
Polymers42,3548
Non-polymers1,18114
Water3,945219
1
D: 26alpha
C: 26beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9656
Polymers10,5882
Non-polymers3764
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-68 kcal/mol
Surface area6090 Å2
MethodPISA
2
G: 26beta
H: 26alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,7444
Polymers10,5882
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-22 kcal/mol
Surface area6040 Å2
MethodPISA
3
B: 26alpha
A: 26beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8365
Polymers10,5882
Non-polymers2473
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-37 kcal/mol
Surface area6070 Å2
MethodPISA
4
E: 26beta
F: 26alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9917
Polymers10,5882
Non-polymers4025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-42 kcal/mol
Surface area5980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.893, 78.322, 81.550
Angle α, β, γ (deg.)90.000, 107.970, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 8 molecules DBHFGEAC

#1: Protein
26alpha


Mass: 5255.154 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Protein
26beta


Mass: 5333.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 4 types, 233 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate, pH 4.6

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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: Apr 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→39.16 Å / Num. obs: 72542 / % possible obs: 100 % / Redundancy: 6.9 % / CC1/2: 1 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.02 / Rrim(I) all: 0.052 / Net I/σ(I): 15.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.7-1.7371.071.730220.790.4352.793100
9-39.166.60.02175.241110.0080.02398.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CC-HP1.0

Resolution: 1.7→39.16 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 4.596 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2122 2926 5.1 %RANDOM
Rwork0.1927 ---
obs0.1937 57178 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.11 Å2 / Biso mean: 33.738 Å2 / Biso min: 19.34 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å2-0 Å21.15 Å2
2---0.79 Å2-0 Å2
3----0.57 Å2
Refinement stepCycle: final / Resolution: 1.7→39.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2892 0 70 219 3181
Biso mean--60.08 44.3 -
Num. residues----397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123065
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163084
X-RAY DIFFRACTIONr_angle_refined_deg1.621.6294123
X-RAY DIFFRACTIONr_angle_other_deg0.5441.5647231
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.625421
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.95510615
X-RAY DIFFRACTIONr_chiral_restr0.0810.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023315
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02485
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 225 -
Rwork0.291 3958 -
all-4183 -
obs--99.76 %
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)
10.57560.3554-0.5831.1338-0.70990.87890.03350.22230.0396-0.09450.01760.03480.1084-0.1664-0.05110.08920.0175-0.00060.12260.00530.0117.1322-25.277522.3976
20.22180.3021-0.13090.8113-0.50840.51840.0532-0.01770.05630.052-0.06350.06930.03630.09070.01040.0495-0.00610.00630.06030.00090.057741.9802-14.683937.0701
30.3616-0.6358-0.061.52090.68371.0849-0.0275-0.0521-0.03170.09870.0912-0.0436-0.0826-0.0185-0.06380.11740.0425-0.03480.0420.01690.054214.428911.025615.9727
40.1384-0.3483-0.25471.26050.84730.77750.0218-0.01030.0337-0.1344-0.1137-0.05480.0367-0.0330.09190.09460.04540.07350.06590.00870.103732.1447-17.44141.9596
50.013-0.02830.03320.5961-0.40330.29160.00110.02620.0305-0.0894-0.0635-0.01910.05170.06730.06240.0292-0.0222-0.01070.08350.03220.101645.2976-14.251929.0037
60.2601-0.36810.46430.5322-0.67350.85310.03120.0221-0.0227-0.0213-0.01690.01720.02490.0267-0.01430.04940.0433-0.01070.05470.00370.04112.381610.5717.7188
70.110.0061-0.06860.07990.21320.66160.0137-0.00420.01640.0285-0.032-0.00120.0722-0.10150.01830.0538-0.0403-0.00930.0523-0.00420.048918.622-25.765530.6542
80.14250.0291-0.23770.68440.25120.5659-0.0053-0.1099-0.0298-0.0373-0.18250.18160.04760.11510.18780.03240.02960.03170.1305-0.01550.106829.2022-16.890210.3175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D0 - 49
2X-RAY DIFFRACTION2G1 - 48
3X-RAY DIFFRACTION3B0 - 50
4X-RAY DIFFRACTION4E0 - 48
5X-RAY DIFFRACTION5H1 - 49
6X-RAY DIFFRACTION6A0 - 49
7X-RAY DIFFRACTION7C0 - 50
8X-RAY DIFFRACTION8F0 - 48

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