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- PDB-9jix: Crystal structure of de novo designed ATPase, PL2x4_2 -

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Basic information

Entry
Database: PDB / ID: 9jix
TitleCrystal structure of de novo designed ATPase, PL2x4_2
ComponentsDe Novo Designed ATPase, PL2x4_2
KeywordsDE NOVO PROTEIN / De Novo Designed Protein / ATP hydrolase / P-loop motif
Function / homologyACETATE ION / AMMONIUM ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsKosugi, T. / Tanabe, M. / Koga, N.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)18H05420 Japan
Japan Science and TechnologyJPMJPR20E6 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101071 Japan
CitationJournal: Protein Sci. / Year: 2025
Title: De novo design of ATPase based on a blueprint optimized for harboring the P-loop motif.
Authors: Kosugi, T. / Tanabe, M. / Koga, N.
History
DepositionSep 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De Novo Designed ATPase, PL2x4_2
C: De Novo Designed ATPase, PL2x4_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5079
Polymers33,9972
Non-polymers5097
Water34219
1
A: De Novo Designed ATPase, PL2x4_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2906
Polymers16,9991
Non-polymers2915
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: De Novo Designed ATPase, PL2x4_2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2173
Polymers16,9991
Non-polymers2182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.663, 77.663, 101.535
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+2/3
#3: -x+y,-x,z+1/3
#4: x-y,-y,-z+1/3
#5: -x,-x+y,-z+2/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-1201-

NH4

21A-1307-

HOH

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Components

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Protein , 1 types, 2 molecules AC

#1: Protein De Novo Designed ATPase, PL2x4_2


Mass: 16998.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 5 types, 26 molecules

#2: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4N
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Sodium Acetate (pH 4.5), 2.0 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.29→40.52 Å / Num. obs: 16444 / % possible obs: 100 % / Redundancy: 9.8 % / Biso Wilson estimate: 58.16 Å2 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.063 / Net I/σ(I): 18.3
Reflection shellResolution: 2.29→2.37 Å / Rmerge(I) obs: 0.959 / Num. unique obs: 1569 / CC1/2: 0.785 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: designed model

Resolution: 2.29→40.52 Å / SU ML: 0.354 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 35.846
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2601 845 5.15 %
Rwork0.2369 15565 -
obs0.2382 16410 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.38 Å2
Refinement stepCycle: LAST / Resolution: 2.29→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 31 19 2347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01092352
X-RAY DIFFRACTIONf_angle_d1.60213182
X-RAY DIFFRACTIONf_chiral_restr0.1021392
X-RAY DIFFRACTIONf_plane_restr0.007413
X-RAY DIFFRACTIONf_dihedral_angle_d16.8557932
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.430.29921160.28922559X-RAY DIFFRACTION99.93
2.43-2.620.34071330.26272556X-RAY DIFFRACTION100
2.62-2.880.30661410.30632557X-RAY DIFFRACTION100
2.89-3.30.32661400.26152582X-RAY DIFFRACTION99.96
3.3-4.160.26461660.23362576X-RAY DIFFRACTION100
4.16-40.520.221490.21212735X-RAY DIFFRACTION99.9

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