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- PDB-4d48: Crystal Structure of glucose-1-phosphate uridylyltransferase GalU... -

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Basic information

Entry
Database: PDB / ID: 4d48
TitleCrystal Structure of glucose-1-phosphate uridylyltransferase GalU from Erwinia amylovora.
ComponentsGLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
KeywordsTRANSFERASE / AMYLOVORAN BIOSYNTHESIS / UDP-GLUCOSE / FIRE BLIGHT
Function / homology
Function and homology information


UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / biosynthetic process
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase, bacterial/archaeal-type / Nucleotidyl transferase domain / Nucleotidyl transferase / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesERWINIA AMYLOVORA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å
AuthorsToccafondi, M. / Wuerges, J. / Cianci, M. / Benini, S.
Citation
Journal: Biochim. Biophys. Acta / Year: 2017
Title: Glucose-1-phosphate uridylyltransferase from Erwinia amylovora: Activity, structure and substrate specificity.
Authors: Benini, S. / Toccafondi, M. / Rejzek, M. / Musiani, F. / Wagstaff, B.A. / Wuerges, J. / Cianci, M. / Field, R.A.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Expression, purification, crystallization and preliminary X-ray analysis of glucose-1-phosphate uridylyltransferase (GalU) from Erwinia amylovora.
Authors: Toccafondi, M. / Cianci, M. / Benini, S.
History
DepositionOct 27, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 14, 2018Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
B: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE


Theoretical massNumber of molelcules
Total (without water)65,8462
Polymers65,8462
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-45.9 kcal/mol
Surface area24490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.673, 80.673, 169.182
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.466, 0.8848, -0.001262), (0.8848, -0.466, -0.004734), (-0.004776, 0.00109, -1)
Vector: -20.02, 33.17, 0.06046)

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Components

#1: Protein GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE


Mass: 32922.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ERWINIA AMYLOVORA (bacteria) / Strain: CFBP1430 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: D4I3X5, UTP-glucose-1-phosphate uridylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 2.57 Å3/Da / Density % sol: 52.09 % / Description: NONE
Crystal growpH: 8.5
Details: 2M AMMONIUM SULFATE, 0.1 M TRIS PH 8.5, 5% ETHYLENE GLYCOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.033
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2014
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.46→66.66 Å / Num. obs: 12434 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 8.7 % / Biso Wilson estimate: 57.06 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.1
Reflection shellResolution: 2.46→2.56 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.4 / % possible all: 94.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
SCALAdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E3D

2e3d


Resolution: 2.46→64.66 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.909 / SU B: 28.167 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.658 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED. THE FOLLOWING RESIDUES WERE DISORDERED 1-4, 84-87, 233-238, 299-302
RfactorNum. reflection% reflectionSelection details
Rfree0.27311 1137 5.1 %RANDOM
Rwork0.24352 ---
obs0.24506 21211 99.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 70.542 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0.25 Å20 Å2
2---0.25 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.46→64.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4345 0 0 14 4359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194425
X-RAY DIFFRACTIONr_bond_other_d0.0040.024330
X-RAY DIFFRACTIONr_angle_refined_deg1.5141.9776012
X-RAY DIFFRACTIONr_angle_other_deg0.991310007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5145563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74125.819177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.93815772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7591514
X-RAY DIFFRACTIONr_chiral_restr0.0890.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214935
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02875
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.462→2.526 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 89 -
Rwork0.337 1401 -
obs--89.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.90470.25090.67751.0240.13092.36210.04260.52770.0229-0.2226-0.04960.1908-0.0276-0.02860.00710.127-0.06830.00130.3537-0.09490.06662.727729.3768-17.7109
22.94020.46260.88671.4716-0.55823.71060.031-0.3677-0.52760.3201-0.0032-0.04950.2614-0.2599-0.02780.1889-0.08380.05760.2320.01630.12317.386521.841417.7761
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 298
2X-RAY DIFFRACTION2B5 - 298

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