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- PDB-8gqp: Complex of D-protein binder D-19437 and L-target L-Pep-1 -

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Basic information

Entry
Database: PDB / ID: 8gqp
TitleComplex of D-protein binder D-19437 and L-target L-Pep-1
Components
  • D-binder
  • L-pep1
KeywordsDE NOVO PROTEIN / D-protein / heterochiral protein complex / protein-protein interaction / mirror-image / de novo / design
Function / homologypolypeptide(D) / polypeptide(D) (> 10)
Function and homology information
Biological speciesartificial sequences (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLiang, M.F. / Li, S.C. / Wang, T.Y. / Liu, L. / Lu, P.L.
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
DepositionAug 30, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2024Group: Database references / Refinement description / Category: citation / citation_author / struct_ncs_dom_lim
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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / 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
A: D-binder
B: L-pep1
C: D-binder
D: L-pep1


Theoretical massNumber of molelcules
Total (without water)19,5034
Polymers19,5034
Non-polymers00
Water1,44180
1
A: D-binder
B: L-pep1


Theoretical massNumber of molelcules
Total (without water)9,7512
Polymers9,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1330 Å2
ΔGint-15 kcal/mol
Surface area5140 Å2
MethodPISA
2
C: D-binder
D: L-pep1


Theoretical massNumber of molelcules
Total (without water)9,7512
Polymers9,7512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-15 kcal/mol
Surface area5140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.395, 82.282, 35.323
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-104-

HOH

21C-130-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain C
12(chain B and resid 1 through 18)
22(chain D and (resid 1 through 17 or (resid 18...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11DLEDLEDSNDSNchain AAA1 - 621 - 62
21DLEDLEDSNDSNchain CCC1 - 621 - 62
12ASPASPLYSLYS(chain B and resid 1 through 18)BB1 - 181 - 18
22ASPASPLYSLYS(chain D and (resid 1 through 17 or (resid 18...DD1 - 181 - 18

NCS ensembles :
ID
1
2

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Components

#1: Protein D-binder


Mass: 7298.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: D-type binder / Source: (synth.) artificial sequences (others)
#2: Protein/peptide L-pep1


Mass: 2452.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / 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 Å3/Da / Density % sol: 38.62 %
Description: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.9
Details: 20%(w/v) PEG 8000, 100mM Tris base/Hydrochloric acid pH7.9, 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: Aug 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→24.4 Å / Num. obs: 10862 / % possible obs: 98.9 % / Redundancy: 4.2 % / Biso Wilson estimate: 22.82 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.028 / Rrim(I) all: 0.059 / Χ2: 0.918 / Net I/av σ(I): 15.44 / Net I/σ(I): 11.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.10.3964560.9040.2560.4750.94588
2.03-2.073.60.365140.9280.2140.4211.00193.8
2.07-2.114.10.285220.9650.1540.3210.9899.1
2.11-2.154.30.2345270.9720.1260.2670.9298.1
2.15-2.24.40.25580.9840.1070.2280.932100
2.2-2.254.40.1615140.9870.0860.1830.902100
2.25-2.314.40.1645430.9840.0870.1860.94100
2.31-2.374.40.1345580.9880.0720.1530.997100
2.37-2.444.40.1185270.9930.0630.1340.894100
2.44-2.524.40.1125610.9950.0590.1270.947100
2.52-2.614.30.0915250.9950.0490.1030.895100
2.61-2.714.40.0845620.9960.0440.0950.872100
2.71-2.844.30.0675330.9960.0360.0770.846100
2.84-2.994.40.0575540.9980.0310.0650.823100
2.99-3.174.30.0515600.9980.0280.0580.81100
3.17-3.424.30.0395470.9990.0210.0440.843100
3.42-3.764.20.0335660.9990.0180.0371.09899.8
3.76-4.314.10.0275640.9990.0150.0310.955100
4.31-5.433.90.0265760.9990.0150.030.97699.8
5.43-24.33.30.0266250.9980.0180.0320.79998.4

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-20007.8data scaling
PDB_EXTRACT3.27data extraction
HKL-20007.8data reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.4 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0.46 / Phase error: 26.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 705 4.78 %
Rwork0.2188 14033 -
obs0.2192 10862 72.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.84 Å2 / Biso mean: 26.8324 Å2 / Biso min: 12.87 Å2
Refinement stepCycle: final / Resolution: 2→24.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 0 80 1415
Biso mean---30.68 -
Num. residues----161
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A438X-RAY DIFFRACTION13.581TORSIONAL
12C438X-RAY DIFFRACTION13.581TORSIONAL
21B164X-RAY DIFFRACTION13.581TORSIONAL
22D164X-RAY DIFFRACTION13.581TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.160.2691880.2528186048
2.16-2.370.25931090.2225217556
2.37-2.720.23291410.2148262668
2.72-3.420.24711580.226362093
3.42-24.40.20672090.2109375297
Refinement TLS params.Method: refined / Origin x: 13.1098 Å / Origin y: 2.4249 Å / Origin z: 9.1033 Å
111213212223313233
T0.1208 Å20.0051 Å20.0255 Å2-0.1595 Å20.0126 Å2--0.1148 Å2
L1.1194 °2-0.3423 °2-0.1042 °2-3.7255 °20.1824 °2--0.3836 °2
S-0.0325 Å °0.0341 Å °-0.0101 Å °0.109 Å °0.0597 Å °0.3556 Å °0.0194 Å °-0.1113 Å °-0.0356 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 62
2X-RAY DIFFRACTION1allB1 - 19
3X-RAY DIFFRACTION1allC1 - 62
4X-RAY DIFFRACTION1allD1 - 18
5X-RAY DIFFRACTION1allS1 - 80

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