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- PDB-3r3i: Crystal Structure of C-terminal truncation of UDP-glucose Pyropho... -

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Basic information

Entry
Database: PDB / ID: 3r3i
TitleCrystal Structure of C-terminal truncation of UDP-glucose Pyrophosphorylase of Homo sapiens
ComponentsUTP--glucose-1-phosphate uridylyltransferase
KeywordsTRANSFERASE / Rossmann fold / beta barrel / nucleotidyltransferase
Function / homology
Function and homology information


pyrimidine ribonucleotide binding / glucose 1-phosphate metabolic process / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis ...pyrimidine ribonucleotide binding / glucose 1-phosphate metabolic process / Formation of the active cofactor, UDP-glucuronate / UTP-glucose-1-phosphate uridylyltransferase / UTP:glucose-1-phosphate uridylyltransferase activity / UDP-glucose metabolic process / glucose binding / glycogen biosynthetic process / glycogen metabolic process / Glycogen synthesis / brain development / extracellular exosome / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex ...UTP--glucose-1-phosphate uridylyltransferase / UDPGP family / UTP--glucose-1-phosphate uridylyltransferase / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / 3 Solenoid / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.57 Å
AuthorsZheng, X. / Yu, Q.
CitationJournal: To be Published
Title: Crystal Structure of UDP-glucose Pyrophosphorylase of Homo sapiens
Authors: Zheng, X. / Yu, Q.
History
DepositionMar 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UTP--glucose-1-phosphate uridylyltransferase
B: UTP--glucose-1-phosphate uridylyltransferase
C: UTP--glucose-1-phosphate uridylyltransferase
D: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)236,7384
Polymers236,7384
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)59,1841
Polymers59,1841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)59,1841
Polymers59,1841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)59,1841
Polymers59,1841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: UTP--glucose-1-phosphate uridylyltransferase


Theoretical massNumber of molelcules
Total (without water)59,1841
Polymers59,1841
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)140.266, 140.266, 315.284
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein
UTP--glucose-1-phosphate uridylyltransferase / UDP-glucose pyrophosphorylase / UDPGP / UGPase


Mass: 59184.402 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UGP2, UGP1 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q16851, UTP-glucose-1-phosphate uridylyltransferase

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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: 3.78 Å3/Da / Density % sol: 67.48 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: magnesium sulfate, PEG3350, glycerol, HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1
DetectorType: MAR / Detector: CCD / Date: Oct 31, 2010
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.566→19.981 Å / Num. all: 43409 / Num. obs: 42839 / % possible obs: 97.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.9 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 3.566→3.61 Å / Rmerge(I) obs: 0.649 / % possible all: 61.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0102refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementStarting model: PDB ENTRY 3R2W

3r2w


Resolution: 3.57→19.98 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 91.284 / SU ML: 0.621 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.603 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2862 2162 5 %RANDOM
Rwork0.2326 40677 --
obs0.2353 42839 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.14 Å2 / Biso mean: 175.894 Å2 / Biso min: 2.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0.33 Å20 Å2
2---0.66 Å20 Å2
3---1 Å2
Refinement stepCycle: LAST / Resolution: 3.57→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13580 0 0 0 13580
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02213821
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.96718839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47751803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.66725.018558
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.115152161
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6581554
X-RAY DIFFRACTIONr_chiral_restr0.1020.22280
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02110357
X-RAY DIFFRACTIONr_mcbond_it0.4911.59041
X-RAY DIFFRACTIONr_mcangle_it0.938214515
X-RAY DIFFRACTIONr_scbond_it1.1534780
X-RAY DIFFRACTIONr_scangle_it2.0494.54324
LS refinement shellResolution: 3.566→3.656 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 131 -
Rwork0.262 2583 -
all-2714 -
obs--87.92 %
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)
13.7091.0187-0.54922.3592-0.51889.2448-0.1584-0.9461-0.05150.0566-0.28920.51040.7426-1.15230.44761.4748-0.49590.06031.44-0.29940.6779-55.452-44.70641.626
22.64831.5318-0.8894.2174-0.8793.6808-0.17440.3485-0.1407-1.1430.03420.01770.65210.00920.14022.3073-0.8566-0.37830.97210.10740.5014-20.512-18.835-24.28
34.8668-2.74881.51185.3255-1.38013.5509-0.08510.49481.5872-0.7676-0.2890.9994-1.2082-1.08390.37412.3163-0.0516-0.55921.7762-0.06841.8012-75.449-34.247-2.937
41.7258-0.39330.96213.3032-1.14382.77610.106-0.1567-0.1031-0.0882-0.3207-0.31060.27320.58120.21471.6786-0.7205-0.19881.19610.1680.3282-40.093-99.65920.827
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 489
2X-RAY DIFFRACTION2B7 - 489
3X-RAY DIFFRACTION3C16 - 489
4X-RAY DIFFRACTION4D11 - 489

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