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- PDB-5zer: UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Sy... -

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Basic information

Entry
Database: PDB / ID: 5zer
TitleUDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - BH2 complex form
ComponentsUDP-glucose:tetrahydrobiopterin glucosyltransferase
KeywordsTRANSFERASE / Tetrahydrobiopterin / Pteridine glycosyltransferase / Pteridine glycosides
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding
Similarity search - Function
: / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7,8-DIHYDROBIOPTERIN / UDP-glucose:tetrahydrobiopterin glucosyltransferase / UDP-glucose:tetrahydrobiopterin glucosyltransferase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsKillivalavan, A. / Lee, K.H.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2012R1A1A2044394 Korea, Republic Of
CitationJournal: To Be Published
Title: UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - BH2 complex form
Authors: Killivalavan, A. / Lee, K.H.
History
DepositionFeb 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-glucose:tetrahydrobiopterin glucosyltransferase
B: UDP-glucose:tetrahydrobiopterin glucosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,3855
Polymers76,8142
Non-polymers5713
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-10 kcal/mol
Surface area28370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.130, 80.000, 53.380
Angle α, β, γ (deg.)90.00, 91.27, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UDP-glucose:tetrahydrobiopterin glucosyltransferase


Mass: 38406.992 Da / Num. of mol.: 2 / Fragment: UNP residues 2-355
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus PCC 7942 (bacteria)
Strain: PCC 7942 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q93EY3, UniProt: Q31LX1*PLUS
#2: Chemical ChemComp-HBI / 7,8-DIHYDROBIOPTERIN


Mass: 239.231 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#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.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Bis-tris, PEG3350, Galactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.39→50 Å / Num. obs: 26482 / % possible obs: 98.4 % / Redundancy: 4.1 % / Net I/σ(I): 8.4
Reflection shellResolution: 2.59→2.63 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZE7

5ze7


Resolution: 2.39→45.71 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.886 / SU B: 14.89 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R: 0.588 / ESU R Free: 0.318 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2858 1396 5 %RANDOM
Rwork0.2151 ---
obs0.21881 26482 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 50.664 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0.46 Å2
2---0.24 Å2-0 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.39→45.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 40 159 5525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195502
X-RAY DIFFRACTIONr_bond_other_d0.0020.025087
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.9777511
X-RAY DIFFRACTIONr_angle_other_deg1.037311760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0985696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02123.547234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.10415797
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8361540
X-RAY DIFFRACTIONr_chiral_restr0.080.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216199
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021139
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_it3.475.0922796
X-RAY DIFFRACTIONr_mcbond_other3.4685.0912795
X-RAY DIFFRACTIONr_mcangle_it5.7197.6173488
X-RAY DIFFRACTIONr_mcangle_other5.7187.6193489
X-RAY DIFFRACTIONr_scbond_it2.9185.3352706
X-RAY DIFFRACTIONr_scbond_other2.9175.3362706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9437.8934024
X-RAY DIFFRACTIONr_long_range_B_refined9.24160.76247
X-RAY DIFFRACTIONr_long_range_B_other9.24160.76247
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.388→2.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 101 -
Rwork0.369 1913 -
obs--97.25 %

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