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- PDB-2ux8: Crystal Structure of Sphingomonas elodea ATCC 31461 Glucose-1- ph... -

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Basic information

Entry
Database: PDB / ID: 2ux8
TitleCrystal Structure of Sphingomonas elodea ATCC 31461 Glucose-1- phosphate uridylyltransferase in Complex with glucose-1-phosphate.
ComponentsGLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
KeywordsTRANSFERASE / UGPG / GALU PYROPHOSPHORYLASE / GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE / NUCLEOTIDYLTRANSFERASE
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
1-O-phosphono-alpha-D-glucopyranose / UTP--glucose-1-phosphate uridylyltransferase
Similarity search - Component
Biological speciesSPHINGOMONAS ELODEA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.65 Å
AuthorsAragao, D. / Fialho, A.M. / Marques, A.R. / Frazao, C. / Sa-Correia, I. / Mitchell, E.P.
Citation
Journal: J.Bacteriol. / Year: 2007
Title: The Complex of Sphingomonas Elodea Atcc 31461 Glucose-1-Phosphate Uridylyltransferase with Glucose-1-Phosphate Reveals a Novel Quaternary Structure, Unique Among Nucleoside Diphosphate-Sugar ...Title: The Complex of Sphingomonas Elodea Atcc 31461 Glucose-1-Phosphate Uridylyltransferase with Glucose-1-Phosphate Reveals a Novel Quaternary Structure, Unique Among Nucleoside Diphosphate-Sugar Pyrophosphorylase Members.
Authors: Aragao, D. / Fialho, A.M. / Marques, A.R. / Mitchell, E.P. / Sa-Correia, I. / Frazao, C.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Cloning, Expression, Purification, Crystallisation and Preliminary Structure Determination of Glucose- 1-Phosphate Uridylyltransferase (Ugpg) Bound to Glucose-1-Phosphate from Sphingomonas Elodea Atcc31461
Authors: Aragao, D. / Marques, A.R. / Frazao, C. / Enguita, F.J. / Carrondo, M.A. / Fialho, A.M. / Sa-Correia, I. / Mitchell, E.P.
History
DepositionMar 27, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 22, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 29, 2023Group: Database references / Structure summary / Category: audit_author / chem_comp / database_2
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 17-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "GA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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
C: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
E: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,79316
Polymers257,7128
Non-polymers2,0818
Water2,864159
1
A: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
B: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
C: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
D: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8968
Polymers128,8564
Non-polymers1,0414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
E: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
F: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
G: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
H: GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,8968
Polymers128,8564
Non-polymers1,0414
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.600, 85.700, 151.800
Angle α, β, γ (deg.)90.00, 105.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GLUCOSE-1-PHOSPHATE URIDYLYLTRANSFERASE


Mass: 32213.961 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: CO-CRYSTALLISED WITH GLUCOSE-1-PHOSPHATE / Source: (gene. exp.) SPHINGOMONAS ELODEA (bacteria) / Plasmid: PUGPG2 BASED ON PWH844 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q5FYV5, UTP-glucose-1-phosphate uridylyltransferase
#2: Sugar
ChemComp-G1P / 1-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-1-PHOSPHATE / 1-O-phosphono-alpha-D-glucose / 1-O-phosphono-D-glucose / 1-O-phosphono-glucose


Type: D-saccharide / Mass: 260.136 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp1PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RECOMBINANT PLASMID CARRIES THE UGPG GENE PRECEDED BY A SEQUENCE CODING FOR SIX HISTIDINE ...THIS RECOMBINANT PLASMID CARRIES THE UGPG GENE PRECEDED BY A SEQUENCE CODING FOR SIX HISTIDINE RESIDUES FOLLOWED BY TWO RESIDUES, A GLYCINE AND A SERINE, BEFORE THE INITIATING METHIONINE.

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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: 2.55 Å3/Da / Density % sol: 51.7 %
Crystal growpH: 4.6
Details: 0.1M AMMONIUM ACETATE, 0.1M SODIUM CITRATE PH=4.6, 15% PEGMME, 5MM G1P, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564, 1.13980
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 12, 2005 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.975641
21.13981
ReflectionResolution: 2.65→102 Å / Num. obs: 85566 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 50.3 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.1
Reflection shellResolution: 2.65→2.67 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.65→74.9 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 884457.43 / Isotropic thermal model: B-GROUP / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: MAXIMUM LIKELIHOOD TARGET USING AMPLITUDES
Details: DIFFERENT NCS RESTRAINS USED FOR MAIN-CHAINS AND FOR SIDE-CHAINS. GROUP B-FACTOR REFINEMENT DOES NOT ALLOW NCS RESTRAINS. DISORDERED REGIONS WERE NOT INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1992 2.6 %SHELLS
Rwork0.245 ---
obs0.245 76179 100 %-
Solvent computationSolvent model: CNS BULK SOLVENT MODEL USED / Bsol: 45.5985 Å2 / ksol: 0.351613 e/Å3
Displacement parametersBiso mean: 54.23 Å2
Baniso -1Baniso -2Baniso -3
1-5.01 Å20 Å2-6.83 Å2
2---5.13 Å20 Å2
3---0.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.38 Å
Luzzati sigma a0.52 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.65→74.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16661 0 128 159 16948
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.84
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINS / Rms dev position: 2 Å / Weight position: 10
LS refinement shellResolution: 2.75→2.77 Å / Total num. of bins used: 39
RfactorNum. reflection% reflection
Rfree0.403 492 0.246 %
Rwork0.346 1500 -
obs--100 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM

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