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- PDB-9iqw: phage HY126 encoded D-arabinose 1,5-diphosphate phosphatase AfhF -

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Basic information

Entry
Database: PDB / ID: 9iqw
Titlephage HY126 encoded D-arabinose 1,5-diphosphate phosphatase AfhF
ComponentsCapsule biosynthesis protein
KeywordsVIRAL PROTEIN / homotetramer
Function / homologyHAD superfamily / HAD-like superfamily / Capsule biosynthesis protein
Function and homology information
Biological speciesPhage #D (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsYu, H. / Lianrong, W.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: structure of bisphosphate phosphatase at 1.64 angstroms resolution
Authors: Yu, H.
History
DepositionJul 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsule biosynthesis protein
B: Capsule biosynthesis protein
C: Capsule biosynthesis protein
E: Capsule biosynthesis protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,08812
Polymers61,6234
Non-polymers4668
Water15,439857
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12060 Å2
ΔGint-86 kcal/mol
Surface area23030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.750, 115.540, 54.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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Components

#1: Protein
Capsule biosynthesis protein / bisphosphate phosphatase


Mass: 15405.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phage #D (virus) / Gene: mogra_227 / Production host: Escherichia (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6B9WR52
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 857 / 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: 2.24 Å3/Da / Density % sol: 45.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 0.2M Mg(HCOO)2.2H2O 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.64→57.84 Å / Num. obs: 74649 / % possible obs: 99.1 % / Redundancy: 11 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22
Reflection shellResolution: 1.64→1.68 Å / Rmerge(I) obs: 0.868 / Num. unique obs: 4996 / CC1/2: 0.648

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→57.77 Å / SU ML: 0.1485 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.1413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 1999 2.68 %RANDOM
Rwork0.1745 72576 --
obs0.1749 74575 98.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.23 Å2
Refinement stepCycle: LAST / Resolution: 1.64→57.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4115 0 28 857 5000
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01124232
X-RAY DIFFRACTIONf_angle_d1.17655733
X-RAY DIFFRACTIONf_chiral_restr0.0738624
X-RAY DIFFRACTIONf_plane_restr0.0108740
X-RAY DIFFRACTIONf_dihedral_angle_d6.5614561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.680.31181300.29764689X-RAY DIFFRACTION90.75
1.68-1.730.27891360.2664969X-RAY DIFFRACTION96.1
1.73-1.780.25271410.23445122X-RAY DIFFRACTION99.3
1.78-1.830.23651420.20375162X-RAY DIFFRACTION99.92
1.83-1.90.17451430.19385193X-RAY DIFFRACTION99.96
1.9-1.980.21171440.19595191X-RAY DIFFRACTION99.96
1.98-2.070.18881430.1785193X-RAY DIFFRACTION99.93
2.07-2.180.21451430.17285226X-RAY DIFFRACTION100
2.18-2.310.19941430.17425199X-RAY DIFFRACTION100
2.31-2.490.1831440.17185217X-RAY DIFFRACTION100
2.49-2.740.19861450.18035267X-RAY DIFFRACTION99.98
2.74-3.140.17921450.17135274X-RAY DIFFRACTION99.98
3.14-3.950.18251470.15175327X-RAY DIFFRACTION100
3.95-57.770.15811530.15315547X-RAY DIFFRACTION99.77

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