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- PDB-7rjf: MOPD-1 mutant-L47W -

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Basic information

Entry
Database: PDB / ID: 7rjf
TitleMOPD-1 mutant-L47W
Components[L47W]MOPD-1
KeywordsANTITUMOR PROTEIN / Synthetic peptide / disulfide-rich peptide / antitumor peptide / peptide mimetic
Function / homologyMALONATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHuawu, Y. / Conan, K.W. / Gordon, J.K. / Brett, M.C. / Yen-Hua, H. / David, J.C.
Funding support Australia, 2items
OrganizationGrant numberCountry
Australian Research Council (ARC)CE200100012 Australia
National Health and Medical Research Council (NHMRC, Australia)APP1136021 Australia
CitationJournal: J.Am.Chem.Soc. / Year: 2021
Title: Rational Design of Potent Peptide Inhibitors of the PD-1:PD-L1 Interaction for Cancer Immunotherapy.
Authors: Yin, H. / Zhou, X. / Huang, Y.H. / King, G.J. / Collins, B.M. / Gao, Y. / Craik, D.J. / Wang, C.K.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 24, 2021Group: 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 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 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
A: [L47W]MOPD-1
B: [L47W]MOPD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,9346
Polymers11,5992
Non-polymers3354
Water45025
1
A: [L47W]MOPD-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,1355
Polymers5,8001
Non-polymers3354
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: [L47W]MOPD-1


Theoretical massNumber of molelcules
Total (without water)5,8001
Polymers5,8001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.377, 41.377, 127.399
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein/peptide [L47W]MOPD-1


Mass: 5799.658 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 200 nL 5 mg/mL peptide + 200 nL 0.1 M zinc chloride, 8% v/v Tacsimate, pH 6.0, 16% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.8→42.47 Å / Num. obs: 10906 / % possible obs: 99.53 % / Redundancy: 2 % / Biso Wilson estimate: 28.89 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.55
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 0.231 / Num. unique obs: 1010

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5JG9 (scaffold)

5jg9


Resolution: 1.8→39.35 Å / SU ML: 0.2044 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 26.6433
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2767 1091 10.01 %
Rwork0.2322 9808 -
obs0.2366 10899 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms802 0 16 25 843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119826
X-RAY DIFFRACTIONf_angle_d1.1341096
X-RAY DIFFRACTIONf_chiral_restr0.0762102
X-RAY DIFFRACTIONf_plane_restr0.007148
X-RAY DIFFRACTIONf_dihedral_angle_d32.632330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.880.34161280.31031148X-RAY DIFFRACTION95.44
1.88-1.980.29461320.26461181X-RAY DIFFRACTION99.85
1.98-2.10.2371330.25551203X-RAY DIFFRACTION99.78
2.1-2.270.28561340.2561205X-RAY DIFFRACTION100
2.27-2.490.26971360.25631220X-RAY DIFFRACTION100
2.5-2.860.30721360.24631230X-RAY DIFFRACTION100
2.86-3.60.31191400.23671256X-RAY DIFFRACTION100
3.6-39.350.24821520.20381365X-RAY DIFFRACTION100

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