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- PDB-7yh8: Crystal structure of a heterochiral protein complex -

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Basic information

Entry
Database: PDB / ID: 7yh8
TitleCrystal structure of a heterochiral protein complex
Components
  • D-Pep-1
  • L-19437
KeywordsDE NOVO PROTEIN / heterochiral / miniprotein / alpha helix / D-protein / D-peptide / mirror-image / de novo / designer
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciessynthetic construct (others)
artificial sequences (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiang, M. / Li, S. / Wang, T. / Liu, L. / Lu, P.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)22137005 China
Ministry of Science and Technology (MoST, China)2020YFA0909200 China
CitationJournal: Cell Res. / Year: 2024
Title: Accurate de novo design of heterochiral protein-protein interactions
Authors: Sun, K. / Li, S. / Zheng, B. / Zhu, Y. / Wang, T. / Liang, M. / Yao, Y. / Zhang, K. / Zhang, J. / Li, H. / Han, D. / Zheng, J. / Coventry, B. / Cao, L. / Baker, D. / Liu, L. / Lu, P.
History
DepositionJul 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: L-19437
B: D-Pep-1
C: L-19437
D: D-Pep-1


Theoretical massNumber of molelcules
Total (without water)19,3694
Polymers19,3694
Non-polymers00
Water1,44180
1
A: L-19437
B: D-Pep-1


Theoretical massNumber of molelcules
Total (without water)9,6842
Polymers9,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-15 kcal/mol
Surface area5200 Å2
MethodPISA
2
C: L-19437
D: D-Pep-1


Theoretical massNumber of molelcules
Total (without water)9,6842
Polymers9,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1310 Å2
ΔGint-16 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.064, 81.922, 35.722
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-110-

HOH

21D-107-

HOH

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Components

#1: Protein L-19437


Mass: 7303.665 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Polypeptide(D) D-Pep-1


Mass: 2380.633 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D amino acid / Source: (synth.) artificial sequences (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% (W/V) PEG 8000, 100mM Tris base/Hydrochloric acid pH8.5, 100mM Magnesium chloride, 20% (V/V) PEG400

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: 100K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 8507 / % possible obs: 98.5 % / Redundancy: 4 % / Biso Wilson estimate: 28.78 Å2 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.028 / Rrim(I) all: 0.058 / Χ2: 0.952 / Net I/σ(I): 12.8 / Num. measured all: 34163
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.243.50.1723980.9750.0970.1991.04291.9
2.24-2.283.70.1893840.9760.1060.2181.02194.3
2.28-2.323.90.193980.9790.1050.2181.09195.2
2.32-2.374.10.1574170.9830.0850.181.07597.9
2.37-2.424.20.1594140.9870.0860.1821.02598.1
2.42-2.484.20.1464150.9880.0790.1661.14199.8
2.48-2.544.20.1374200.9920.0740.1561.11399.8
2.54-2.614.20.1164250.9930.0610.1311.06399.3
2.61-2.694.30.1134120.9880.0610.1291.013100
2.69-2.774.20.1124250.9910.060.1271.0599.3
2.77-2.874.30.0914250.9930.0490.1040.971100
2.87-2.994.20.0774450.9950.0420.0880.99299.8
2.99-3.124.20.0694110.9970.0370.0790.904100
3.12-3.294.10.0554400.9980.030.0630.82899.8
3.29-3.494.20.0454180.9990.0240.0510.815100
3.49-3.7640.0384430.9990.0210.0440.897100
3.76-4.143.90.0334380.9990.0190.0380.888100
4.14-4.743.90.034420.9990.0170.0340.87100
4.74-5.973.70.034650.9990.0180.0350.571100
5.97-503.20.0244720.9990.0140.0280.62895.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000V721.1data scaling
Coot0.9.5model building
HKL-20007.8data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→24.37 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.53 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 430 5.15 %
Rwork0.2022 7921 -
obs0.2047 8351 97.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77 Å2 / Biso mean: 30.953 Å2 / Biso min: 15.63 Å2
Refinement stepCycle: final / Resolution: 2.2→24.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1360 0 0 80 1440
Biso mean---34.59 -
Num. residues----162
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.520.23611240.16942511263595
2.52-3.170.25151580.21726372795100
3.17-24.370.25231480.20522773292199

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