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- PDB-27rq: Crystal structure of the de novo designed miniprotein binder agai... -

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Basic information

Entry
Database: PDB / ID: 27rq
TitleCrystal structure of the de novo designed miniprotein binder against PDL1, Gpx41.
ComponentsDe novo designed miniprotein
KeywordsDE NOVO PROTEIN / Miniprotein binder
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBarik, T. / Kumar, A. / Gaikwad, S.S. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: To Be Published
Title: Crystal structure of the de novo designed miniprotein binder against PDL1, Gpx41.
Authors: Barik, T. / Kumar, A. / Gaikwad, S.S. / Makde, R.D.
History
DepositionJun 9, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 24, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed miniprotein
B: De novo designed miniprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4123
Polymers15,3892
Non-polymers231
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-25 kcal/mol
Surface area6940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.979, 44.979, 157.474
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-176-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid 0 through 3 or resid 5...
d_2ens_1(chain "B" and (resid 0 through 3 or resid 5...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11SERSERSERSERAA0 - 31 - 4
d_12GLUGLUALAALAAA5 - 336 - 34
d_13LEULEUALAALAAA35 - 3936 - 40
d_14THRTHRSERSERAA41 - 7342 - 74
d_21SERSERSERSERBB0 - 31 - 4
d_22GLUGLUALAALABB5 - 336 - 34
d_23LEULEUALAALABB35 - 3936 - 40
d_24THRTHRSERSERBB41 - 7342 - 74

NCS oper: (Code: givenMatrix: (0.508538764499, -0.860917476591, -0.0144714720121), (-0.860878913664, -0.508696518506, 0.010740021824), (-0.0166078599175, 0.00699646767587, -0.999837601028)Vector: 11. ...NCS oper: (Code: given
Matrix: (0.508538764499, -0.860917476591, -0.0144714720121), (-0.860878913664, -0.508696518506, 0.010740021824), (-0.0166078599175, 0.00699646767587, -0.999837601028)
Vector: 11.2717522928, 19.6710365264, 3.75987662849)

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Components

#1: Protein De novo designed miniprotein


Mass: 7694.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pST50Trc2STRHISN / Details (production host): Tan Lab USA / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.42 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 6.5
Details: 0.2M Sodium fluoride, 0.1M BIS-TRIS propane pH-6.5, 20% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.98009 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 30, 2026
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98009 Å / Relative weight: 1
ReflectionResolution: 1.75→44.98 Å / Num. obs: 17283 / % possible obs: 100 % / Redundancy: 24.7 % / Biso Wilson estimate: 22.73 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.021 / Rrim(I) all: 0.108 / Net I/σ(I): 23.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 12.4 % / Rmerge(I) obs: 1.348 / Mean I/σ(I) obs: 2 / Num. unique obs: 923 / CC1/2: 0.74 / Rpim(I) all: 0.384 / Rrim(I) all: 1.411 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.25 Å / SU ML: 0.1688 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.8984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2085 897 5.22 %
Rwork0.17 16296 -
obs0.172 17193 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 1 148 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01611111
X-RAY DIFFRACTIONf_angle_d1.47851505
X-RAY DIFFRACTIONf_chiral_restr0.0794176
X-RAY DIFFRACTIONf_plane_restr0.0085198
X-RAY DIFFRACTIONf_dihedral_angle_d16.9538417
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.604480935487 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.860.27561550.23432628X-RAY DIFFRACTION100
1.86-20.24961450.19092652X-RAY DIFFRACTION99.93
2-2.20.22611490.16152659X-RAY DIFFRACTION99.96
2.2-2.520.23941420.16222714X-RAY DIFFRACTION100
2.52-3.180.22031460.16992733X-RAY DIFFRACTION100
3.18-43.250.16831600.16282910X-RAY DIFFRACTION99.61
Refinement TLS params.Method: refined / Origin x: 23.7059082001 Å / Origin y: -0.546710040143 Å / Origin z: 1.56637310759 Å
111213212223313233
T0.107217580852 Å2-0.00810352801978 Å2-0.0151365367802 Å2-0.130891279994 Å2-0.0114475012686 Å2--0.173123238078 Å2
L1.21925458132 °20.120464630893 °2-0.199389508867 °2-1.48126614354 °2-1.16982486784 °2--4.07211446497 °2
S-0.00237119126813 Å °-0.0535692138015 Å °-0.0217505263711 Å °0.0833652264035 Å °0.00554255807808 Å °-0.0752742247494 Å °-0.160456717019 Å °-0.0538628298252 Å °-0.0144600057738 Å °
Refinement TLS groupSelection details: all

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