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- PDB-5ze7: UDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Sy... -

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Basic information

Entry
Database: PDB / ID: 5ze7
TitleUDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - apo form
ComponentsUDP-glucose:tetrahydrobiopterin glucosyltransferase
KeywordsTRANSFERASE / Tetrahydrobiopterin / UDPglucose / Pteridine glycosyltransferase / Pteridine glycosides / Synechococcus.
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
UDP-glucose:tetrahydrobiopterin glucosyltransferase / UDP-glucose:tetrahydrobiopterin glucosyltransferase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.99 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 - apo 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 1.1Dec 4, 2019Group: Data collection / Category: reflns_shell
Revision 1.2Nov 20, 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
B: UDP-glucose:tetrahydrobiopterin glucosyltransferase
A: UDP-glucose:tetrahydrobiopterin glucosyltransferase


Theoretical massNumber of molelcules
Total (without water)76,5002
Polymers76,5002
Non-polymers00
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1300 Å2
ΔGint-5 kcal/mol
Surface area29300 Å2
Unit cell
Length a, b, c (Å)171.350, 77.992, 53.770
Angle α, β, γ (deg.)90.00, 90.27, 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) / References: UniProt: Q93EY3, UniProt: Q31LX1*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Bis-tris, PEG 3350, Galactose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.979, 0.979,0.964
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 28, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.9641
Reflection
Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Entry-IDDiffraction-IDNet I/σ(I)
1.99-504864299.94.65ZE718.6
1.99-50485771004.75ZE717.8
1.99-50488271004.65ZE716.7
Reflection shellResolution: 1.99→2.02 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 1.99→45.447 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 2458 5.06 %
Rwork0.1853 --
obs0.1872 48623 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→45.447 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5331 0 0 224 5555
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085471
X-RAY DIFFRACTIONf_angle_d1.0437472
X-RAY DIFFRACTIONf_dihedral_angle_d14.1793239
X-RAY DIFFRACTIONf_chiral_restr0.057829
X-RAY DIFFRACTIONf_plane_restr0.007987
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9898-2.02810.27151410.23992480X-RAY DIFFRACTION99
2.0281-2.06950.30121190.22492618X-RAY DIFFRACTION100
2.0695-2.11450.2641450.21532515X-RAY DIFFRACTION100
2.1145-2.16370.23111280.20482592X-RAY DIFFRACTION100
2.1637-2.21780.26561430.20392530X-RAY DIFFRACTION100
2.2178-2.27780.25751280.20252542X-RAY DIFFRACTION100
2.2778-2.34480.24491380.20612593X-RAY DIFFRACTION100
2.3448-2.42050.22061400.20562558X-RAY DIFFRACTION100
2.4205-2.5070.26751440.19572535X-RAY DIFFRACTION100
2.507-2.60730.26811450.19972552X-RAY DIFFRACTION100
2.6073-2.7260.21881460.20272533X-RAY DIFFRACTION100
2.726-2.86970.25921410.21852584X-RAY DIFFRACTION100
2.8697-3.04940.26351080.20442594X-RAY DIFFRACTION100
3.0494-3.28480.23741500.19752562X-RAY DIFFRACTION100
3.2848-3.61530.24691200.18862605X-RAY DIFFRACTION100
3.6153-4.13810.18451370.16252571X-RAY DIFFRACTION100
4.1381-5.21240.18721340.14932588X-RAY DIFFRACTION100
5.2124-45.45920.16171510.15392613X-RAY DIFFRACTION99

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