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- PDB-9lj9: Crystal structure of a bifunctional 3-hexulose-6-phosphate syntha... -

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Basic information

Entry
Database: PDB / ID: 9lj9
TitleCrystal structure of a bifunctional 3-hexulose-6-phosphate synthase/6-phospho-3-hexuloisomerase
Components3-hexulose-6-phosphate synthase
KeywordsISOMERASE / dimer / 3-hexulose-6-phosphate Synthase / Formaldehyde Assimilation / ribulose monophosphate cycle
Function / homology
Function and homology information


hexulose-6-phosphate synthase activity / formaldehyde assimilation via ribulose monophosphate cycle / 3-hexulose-6-phosphate synthase / carbohydrate derivative metabolic process / carbohydrate derivative binding / orotidine-5'-phosphate decarboxylase activity / 'de novo' pyrimidine nucleobase biosynthetic process / isomerase activity / carbohydrate metabolic process
Similarity search - Function
3-hexulose-6-phosphate synthase / 3-hexulose-6-phosphate isomerase / HPS/KGPDC domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family ...3-hexulose-6-phosphate synthase / 3-hexulose-6-phosphate isomerase / HPS/KGPDC domain / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Orotidine 5'-phosphate decarboxylase domain / Orotidine 5'-phosphate decarboxylase / HUMPS family / Orotidine 5'-phosphate decarboxylase / HUMPS family / Ribulose-phosphate binding barrel / Aldolase-type TIM barrel
Similarity search - Domain/homology
3-hexulose-6-phosphate synthase
Similarity search - Component
Biological speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsWang, H. / Feng, Y. / Liu, L. / Li, Y.X. / Ji, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Crystal Structure, Mutations, and Catalytic Properties of 3-Hexulose-6-phosphate Synthase from Pyrococcus horikoshii.
Authors: Li, Y. / Liu, Y. / Ji, Y. / Xu, H. / Wang, H. / Feng, Y. / Liu, L.
History
DepositionJan 14, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: 3-hexulose-6-phosphate synthase
A: 3-hexulose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6116
Polymers93,3712
Non-polymers2414
Water2,954164
1
B: 3-hexulose-6-phosphate synthase
A: 3-hexulose-6-phosphate synthase
hetero molecules

B: 3-hexulose-6-phosphate synthase
A: 3-hexulose-6-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,22312
Polymers186,7414
Non-polymers4818
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area11240 Å2
ΔGint-105 kcal/mol
Surface area61070 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-40 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.923, 205.698, 143.374
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

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Components

#1: Protein 3-hexulose-6-phosphate synthase


Mass: 46685.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: PH1938 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O59601, 3-hexulose-6-phosphate synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.8 M Sodium formate 0.1 M Tris pH7.5 8 % w/v PEG 20,000 8 % v/v PEG 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 4, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.64→33.63 Å / Num. obs: 29508 / % possible obs: 99.74 % / Redundancy: 12.4 % / Biso Wilson estimate: 51.1 Å2 / CC1/2: 0.996 / Net I/σ(I): 8.98
Reflection shellResolution: 2.64→2.734 Å / Num. unique obs: 2861 / CC1/2: 0.578

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
PHENIXphasing
IPCASmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→32.59 Å / SU ML: 0.358 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.7258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2646 1457 4.94 %
Rwork0.2211 28061 -
obs0.2232 29478 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.92 Å2
Refinement stepCycle: LAST / Resolution: 2.64→32.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5486 0 12 164 5662
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425554
X-RAY DIFFRACTIONf_angle_d0.6317490
X-RAY DIFFRACTIONf_chiral_restr0.0468918
X-RAY DIFFRACTIONf_plane_restr0.005934
X-RAY DIFFRACTIONf_dihedral_angle_d14.59832078
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.730.33221370.29752618X-RAY DIFFRACTION94.58
2.73-2.840.32921550.28192774X-RAY DIFFRACTION99.83
2.84-2.970.33771420.26882762X-RAY DIFFRACTION99.93
2.97-3.120.331500.24812827X-RAY DIFFRACTION99.97
3.12-3.320.25981480.242781X-RAY DIFFRACTION99.93
3.32-3.580.26891190.23642828X-RAY DIFFRACTION99.9
3.58-3.930.25811540.20682811X-RAY DIFFRACTION99.93
3.94-4.50.24241270.19522865X-RAY DIFFRACTION99.97
4.5-5.670.2311490.19892844X-RAY DIFFRACTION99.9
5.67-32.590.24771760.20762951X-RAY DIFFRACTION99.78

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