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

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Basic information

Entry
Database: PDB / ID: 5zes
TitleUDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - UDP complex
ComponentsUDP-glucose:tetrahydrobiopterin glucosyltransferase
KeywordsTRANSFERASE / Tetrahydrobiopterin / Pteridine glycosyltransferase / Pteridine glycosides
Function / homology: / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / glycosyltransferase activity / nucleotide binding / URIDINE-5'-DIPHOSPHATE / UDP-glucose:tetrahydrobiopterin glucosyltransferase / UDP-glucose:tetrahydrobiopterin glucosyltransferase
Function and homology information
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.03 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 - UDP complex
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 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)77,0885
Polymers76,5002
Non-polymers5883
Water3,207178
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-11 kcal/mol
Surface area29030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)171.810, 78.698, 53.605
Angle α, β, γ (deg.)90.00, 90.87, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein UDP-glucose:tetrahydrobiopterin glucosyltransferase


Mass: 38249.797 Da / Num. of mol.: 2 / Fragment: UNP residues 2-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (strain 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-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: UDP*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 178 / 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: 2.37 Å3/Da / Density % sol: 48.07 %
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: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979,0.979,0.987
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9871
ReflectionResolution: 2.03→50 Å / Num. obs: 46172 / % possible obs: 99.9 % / Redundancy: 3.8 % / Net I/σ(I): 10
Reflection shellResolution: 2.03→2.07 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.03→29.01 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.418 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23536 2295 5 %RANDOM
Rwork0.18281 ---
obs0.1854 43674 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.088 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0.14 Å2
2--0.1 Å2-0 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.03→29.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5361 0 37 178 5576
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195534
X-RAY DIFFRACTIONr_bond_other_d0.0030.025092
X-RAY DIFFRACTIONr_angle_refined_deg1.9251.9767559
X-RAY DIFFRACTIONr_angle_other_deg1.131311788
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0535702
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.53423.84237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.37115799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7751537
X-RAY DIFFRACTIONr_chiral_restr0.1110.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216240
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021129
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_it3.7043.8152817
X-RAY DIFFRACTIONr_mcbond_other3.6973.8132816
X-RAY DIFFRACTIONr_mcangle_it5.6965.6993516
X-RAY DIFFRACTIONr_mcangle_other5.6985.7013517
X-RAY DIFFRACTIONr_scbond_it4.3914.3542717
X-RAY DIFFRACTIONr_scbond_other4.3884.3542717
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7046.334044
X-RAY DIFFRACTIONr_long_range_B_refined9.69446.4156064
X-RAY DIFFRACTIONr_long_range_B_other9.69346.4246065
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.03→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 169 -
Rwork0.3 3108 -
obs--95.85 %

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