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- PDB-27ah: Crystal structure of the de novo designed miniprotein Gpx15 in th... -

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Basic information

Entry
Database: PDB / ID: 27ah
TitleCrystal structure of the de novo designed miniprotein Gpx15 in the C121 space group.
ComponentsDe novo designed miniprotein
KeywordsDE NOVO PROTEIN / De novo designed miniprotein / RFdiffusion / TIM3
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsBarik, T. / Gayri, S. / 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 Gpx15 in the C121 space group.
Authors: Barik, T. / Gayri, S. / Kumar, A. / Gaikwad, S.S. / Makde, R.D.
History
DepositionMay 22, 2026Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 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


Theoretical massNumber of molelcules
Total (without water)17,6982
Polymers17,6982
Non-polymers00
Water4,197233
1
A: De novo designed miniprotein


Theoretical massNumber of molelcules
Total (without water)8,8491
Polymers8,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: De novo designed miniprotein


Theoretical massNumber of molelcules
Total (without water)8,8491
Polymers8,8491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.098, 34.119, 61.669
Angle α, β, γ (deg.)90.000, 101.492, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
d_1ens_1(chain "A" and (resid -1 through 28 or resid 30...
d_2ens_1(chain "B" and (resid -1 through 28 or resid 30...

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_11GLYGLYALAALAAA-1 - 281 - 30
d_12ALAALALEULEUAA30 - 4132 - 43
d_13GLYGLYALAALAAA43 - 4545 - 47
d_14LYSLYSALAALAAA47 - 8049 - 82
d_21GLYGLYALAALABB-1 - 281 - 30
d_22ALAALALEULEUBB30 - 4132 - 43
d_23GLYGLYALAALABB43 - 4545 - 47
d_24LYSLYSALAALABB47 - 8049 - 82

NCS oper: (Code: givenMatrix: (-0.999052926421, -0.0335800101454, 0.0276700763906), (-0.0305686864947, 0.0891230123742, -0.995551427135), (0.0309645864629, -0.995454404573, -0.0900651031265)Vector: ...NCS oper: (Code: given
Matrix: (-0.999052926421, -0.0335800101454, 0.0276700763906), (-0.0305686864947, 0.0891230123742, -0.995551427135), (0.0309645864629, -0.995454404573, -0.0900651031265)
Vector: 32.7406305735, 15.3590630702, 15.8328446164)

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Components

#1: Protein De novo designed miniprotein


Mass: 8849.075 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
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: 49.18 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 4
Details: 0.1M MIB buffer pH 4, 25% PEG 1500; 31mg/ml miniprotein

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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: 0.97893 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2026 / Details: Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.4→40.72 Å / Num. obs: 33408 / % possible obs: 99.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 13.3 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.023 / Rrim(I) all: 0.064 / Net I/σ(I): 18.8
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.882 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 1627 / CC1/2: 0.778 / Rpim(I) all: 0.348 / Rrim(I) all: 0.949 / % possible all: 96.2

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXphasing
Cootmodel building
PHENIX1.21.2_5419refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→30.22 Å / SU ML: 0.1711 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.7673
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2135 1645 4.93 %
Rwork0.1863 31748 -
obs0.1877 33393 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.46 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 0 235 1475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01521286
X-RAY DIFFRACTIONf_angle_d1.54031721
X-RAY DIFFRACTIONf_chiral_restr0.0845191
X-RAY DIFFRACTIONf_plane_restr0.0118223
X-RAY DIFFRACTIONf_dihedral_angle_d17.8295497
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.987747026872 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.29841460.26292554X-RAY DIFFRACTION97.4
1.44-1.490.25671490.23192569X-RAY DIFFRACTION97.59
1.49-1.540.231330.20512633X-RAY DIFFRACTION98.82
1.54-1.60.28451380.18942618X-RAY DIFFRACTION98.89
1.6-1.680.24011210.18962620X-RAY DIFFRACTION98.95
1.68-1.760.19341470.19292628X-RAY DIFFRACTION99.11
1.76-1.870.20171120.18892673X-RAY DIFFRACTION99.36
1.87-2.020.23161420.18352641X-RAY DIFFRACTION99.29
2.02-2.220.22071400.17252657X-RAY DIFFRACTION99.89
2.22-2.540.20021460.18372661X-RAY DIFFRACTION99.96
2.54-3.20.19961340.19782723X-RAY DIFFRACTION100
3.2-30.220.2011370.1712771X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: 16.6101139421 Å / Origin y: 0.469542884743 Å / Origin z: 14.2120143871 Å
111213212223313233
T0.133952311211 Å2-0.00255416903963 Å2-0.012721207811 Å2-0.0938164679894 Å20.0248764470652 Å2--0.0930670089867 Å2
L0.634776944447 °20.0831148095883 °20.0747970904605 °2-0.640960068739 °20.482701075452 °2--1.12592685659 °2
S0.0169099942444 Å °-0.0436737335421 Å °-0.0283052475431 Å °0.0385655010865 Å °-0.00317151355364 Å °-0.0122321871237 Å °-0.00707970504658 Å °-0.0605572850602 Å °-0.013031246613 Å °
Refinement TLS groupSelection details: all

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