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

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Basic information

Entry
Database: PDB / ID: 5zfk
TitleUDP Glucose alpha tetrahydrobiopterin glycosyltransferase from Synechococcus species PCC 7942 - UDP-BH2 complex
Components(UDP-glucose:tetrahydrobiopterin glucosyltransferase) x 2
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
7,8-DIHYDROBIOPTERIN / URIDINE-5'-DIPHOSPHATE / UDP-glucose:tetrahydrobiopterin glucosyltransferase / UDP-glucose:tetrahydrobiopterin glucosyltransferase
Similarity search - Component
Biological speciesSynechococcus elongatus PCC 7942 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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
DepositionMar 6, 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 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)77,5395
Polymers76,6572
Non-polymers8833
Water7,548419
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-16 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.370, 79.984, 53.827
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-730-

HOH

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Components

#1: Protein UDP-glucose:tetrahydrobiopterin glucosyltransferase


Mass: 38406.992 Da / Num. of mol.: 1 / 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: Protein UDP-glucose:tetrahydrobiopterin glucosyltransferase


Mass: 38249.797 Da / Num. of mol.: 1 / Fragment: UNP residues 2-354
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
#3: 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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.36 Å3/Da / Density % sol: 47.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: Bis-tris, PEG3350

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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: 1.75→50 Å / Num. obs: 71852 / % possible obs: 99.2 % / Redundancy: 3.7 % / Net I/σ(I): 14.5
Reflection shellResolution: 1.75→1.78 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: 1.75→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.435 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19987 3646 5.1 %RANDOM
Rwork0.1586 ---
obs0.16072 68206 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å2-0.05 Å2
2--0.15 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5377 0 59 419 5855
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195597
X-RAY DIFFRACTIONr_bond_other_d0.0020.025145
X-RAY DIFFRACTIONr_angle_refined_deg2.0391.9817655
X-RAY DIFFRACTIONr_angle_other_deg1.132311908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0975711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40323.75240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51815809
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8991539
X-RAY DIFFRACTIONr_chiral_restr0.1330.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216318
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021155
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_it2.4972.6092832
X-RAY DIFFRACTIONr_mcbond_other2.4962.6072831
X-RAY DIFFRACTIONr_mcangle_it3.4443.8963538
X-RAY DIFFRACTIONr_mcangle_other3.4443.8973539
X-RAY DIFFRACTIONr_scbond_it3.6783.0162765
X-RAY DIFFRACTIONr_scbond_other3.6793.0162764
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3964.3644115
X-RAY DIFFRACTIONr_long_range_B_refined6.63731.9926356
X-RAY DIFFRACTIONr_long_range_B_other6.57731.7386276
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.747→1.792 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 240 -
Rwork0.257 4750 -
obs--93.39 %

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