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- PDB-9ix8: Crystallization and structural characterization of phosphopentomu... -

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Basic information

Entry
Database: PDB / ID: 9ix8
TitleCrystallization and structural characterization of phosphopentomutase from the hyperthermophilic archaeon Thermococcus kodakarensis
ComponentsPhosphopentomutase
KeywordsISOMERASE / Phosphopentomutase / Thermococcus kodakarensis / Hyperthermophilic archaea / Phosphohexomutase homologue
Function / homology
Function and homology information


phosphoglucosamine mutase activity / phosphopentomutase / phosphopentomutase activity / phosphomannomutase activity / carbohydrate metabolic process / magnesium ion binding
Similarity search - Function
Phosphoglucosamine mutase, archaeal type / : / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II ...Phosphoglucosamine mutase, archaeal type / : / Alpha-D-phosphohexomutase, C-terminal / Phosphoglucomutase/phosphomannomutase, C-terminal domain / Alpha-D-phosphohexomutase superfamily / Alpha-D-phosphohexomutase, conserved site / Phosphoglucomutase and phosphomannomutase phosphoserine signature. / Alpha-D-phosphohexomutase, alpha/beta/alpha domain II / Alpha-D-phosphohexomutase, alpha/beta/alpha domain III / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain III / Alpha-D-phosphohexomutase, alpha/beta/alpha domain I / Alpha-D-phosphohexomutase, alpha/beta/alpha I/II/III / Alpha-D-phosphohexomutase, C-terminal domain superfamily / Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain I
Similarity search - Domain/homology
Chem-7PE / Phosphopentomutase
Similarity search - Component
Biological speciesThermococcus kodakarensis KOD1 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsNaz, Z. / Lubkowski, T.J. / Saleem, M. / Rahman, M. / Wlodawer, A. / Rashid, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Int J Mol Sci / Year: 2024
Title: Biophysical Characterization of a Novel Phosphopentomutase from the Hyperthermophilic Archaeon Thermococcus kodakarensis .
Authors: Naz, Z. / Lubkowski, J. / Saleem, M. / Aslam, M. / Rahman, M. / Wlodawer, A. / Rashid, N.
History
DepositionJul 26, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2025Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphopentomutase
B: Phosphopentomutase
C: Phosphopentomutase
D: Phosphopentomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,5807
Polymers197,8674
Non-polymers7133
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-49 kcal/mol
Surface area63850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.772, 97.575, 128.150
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphopentomutase / PPM


Mass: 49466.691 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermococcus kodakarensis KOD1 (archaea)
Gene: TK1777, Tko0866 / Plasmid: pNZPi / Details (production host): pET-21a(+)-His6-TEV-Tk1777 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIPL / References: UniProt: Q6I7B6, phosphopentomutase
#2: Chemical ChemComp-7PE / 2-(2-(2-(2-(2-(2-ETHOXYETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHOXY)ETHANOL / POLYETHYLENE GLYCOL FRAGMENT


Mass: 310.384 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H30O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% v/v PEG300, 10% v/v Glycerol, 0.1 M Tris-HCl- pH 8.5, 5% w/v PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.9 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.9 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 77057 / % possible obs: 98.9 % / Redundancy: 7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.135 / Net I/σ(I): 10.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.39-2.536.81.0391.57121370.70.597
2.53-2.710.652115700.8730.135
2.71-2.920.401108520.9470.433
2.92-3.20.252100160.9770.272
3.2-3.580.14291110.9920.155
3.58-4.130.08480800.9960.091
4.13-5.050.05968980.9980.063
5.05-7.10.06253320.9980.067

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.39→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.344 / SU ML: 0.215 / Cross valid method: THROUGHOUT / ESU R: 0.44 / ESU R Free: 0.29 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27378 2310 3 %RANDOM
Rwork0.20111 ---
obs0.2033 74699 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.494 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20.53 Å2
2--0.49 Å20 Å2
3----1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.39→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13803 0 48 419 14270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01314151
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713713
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.64219163
X-RAY DIFFRACTIONr_angle_other_deg1.2661.57831714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.01251787
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.99621.525708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.151152451
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.91515109
X-RAY DIFFRACTIONr_chiral_restr0.0810.21819
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215779
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022940
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.6125.0287136
X-RAY DIFFRACTIONr_mcbond_other4.6085.0287135
X-RAY DIFFRACTIONr_mcangle_it6.6757.538915
X-RAY DIFFRACTIONr_mcangle_other6.6767.5318916
X-RAY DIFFRACTIONr_scbond_it5.2225.6977015
X-RAY DIFFRACTIONr_scbond_other5.2215.6977016
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.9168.27810245
X-RAY DIFFRACTIONr_long_range_B_refined10.83358.6915408
X-RAY DIFFRACTIONr_long_range_B_other10.83858.68815384
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.39→2.452 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 166 -
Rwork0.373 5367 -
obs--97.04 %

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