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- PDB-9jwt: De novo designed D-allose binding protein based on 1rpj -

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Basic information

Entry
Database: PDB / ID: 9jwt
TitleDe novo designed D-allose binding protein based on 1rpj
ComponentsMSD3-holo
KeywordsDE NOVO PROTEIN / De novo designed D-allose binding protein based on 1rpj
Function / homologybeta-D-allopyranose
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsWang, X. / Liu, Y.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: De novo designed D-allose binding protein based on 1rpj
Authors: Wang, X. / Liu, Y.
History
DepositionOct 10, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MSD3-holo
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0412
Polymers30,8611
Non-polymers1801
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.496, 43.038, 143.291
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein MSD3-holo


Mass: 30861.281 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli B (bacteria)
#2: Sugar ChemComp-ALL / beta-D-allopyranose / beta-D-allose / D-allose / allose / D-ALLOPYRANOSE


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DAllpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-allopyranoseCOMMON NAMEGMML 1.0
b-D-AllpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
AllSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.02 Å3/Da / Density % sol: 39.2 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: condition:25% w/v Polythylene glycol 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 1.6→71.65 Å / Num. obs: 33452 / % possible obs: 98.7 % / Redundancy: 5.4 % / Biso Wilson estimate: 17.08 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.068 / Net I/σ(I): 9.5
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 0.867 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 1598 / CC1/2: 0.791 / Rpim(I) all: 0.589

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→38.97 Å / SU ML: 0.1791 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1605
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2169 1694 5.07 %
Rwork0.1853 31688 -
obs0.1869 33382 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.19 Å2
Refinement stepCycle: LAST / Resolution: 1.6→38.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2128 0 12 288 2428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00552169
X-RAY DIFFRACTIONf_angle_d0.80162937
X-RAY DIFFRACTIONf_chiral_restr0.0508351
X-RAY DIFFRACTIONf_plane_restr0.0065376
X-RAY DIFFRACTIONf_dihedral_angle_d14.8308800
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.650.28881510.26772547X-RAY DIFFRACTION97.05
1.65-1.70.28261480.25512577X-RAY DIFFRACTION97.74
1.7-1.760.27411620.23752559X-RAY DIFFRACTION97.7
1.76-1.830.28071260.22832589X-RAY DIFFRACTION97.63
1.83-1.910.24471370.21532618X-RAY DIFFRACTION98.22
1.91-2.020.22481330.18652616X-RAY DIFFRACTION98.21
2.02-2.140.25751320.18672635X-RAY DIFFRACTION98.4
2.14-2.310.23221470.18032599X-RAY DIFFRACTION98.21
2.31-2.540.24251300.18742713X-RAY DIFFRACTION98.99
2.54-2.910.21771370.1862675X-RAY DIFFRACTION99.19
2.91-3.660.19451340.16572750X-RAY DIFFRACTION99.35
3.66-38.970.17011570.16252810X-RAY DIFFRACTION97.7

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