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- PDB-4xsu: Crystal structure of Anabaena Alr3699/HepE in complex with UDP an... -

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Basic information

Entry
Database: PDB / ID: 4xsu
TitleCrystal structure of Anabaena Alr3699/HepE in complex with UDP and glucose
ComponentsAlr3699 protein
KeywordsTRANSFERASE / GT-B fold / glycosyltransferase
Function / homology
Function and homology information


glycosyltransferase activity / nucleotide binding
Similarity search - Function
Glycosyltransferase Family 4 / : / Glycosyltransferase subfamily 4-like, N-terminal domain / Glycosyl transferase, family 1 / Glycosyl transferases group 1
Similarity search - Domain/homology
alpha-D-glucopyranose / URIDINE-5'-DIPHOSPHATE / Alr3699 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsWang, X.P. / Dai, Y.N. / Jiang, Y.L. / Cheng, W. / Chen, Y.X. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31370757 China
CitationJournal: Glycobiology / Year: 2016
Title: Structural and enzymatic analyses of a glucosyltransferase Alr3699/HepE involved in Anabaena heterocyst envelop polysaccharide biosynthesis
Authors: Wang, X.P. / Jiang, Y.L. / Dai, Y.N. / Cheng, W. / Chen, Y. / Zhou, C.Z.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 13, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _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: Alr3699 protein
A: Alr3699 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,87216
Polymers84,7472
Non-polymers2,12514
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-132 kcal/mol
Surface area29580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.991, 130.991, 156.327
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein / Sugars , 2 types, 4 molecules BA

#1: Protein Alr3699 protein


Mass: 42373.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (strain PCC 7120 / UTEX 2576) (bacteria)
Strain: PCC 7120 / UTEX 2576 / Gene: alr3699 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8YQW3, Transferases; Glycosyltransferases; Hexosyltransferases
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 231 molecules

#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.57 Å3/Da / Density % sol: 73.08 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.5 M Li2SO4, 0.1 M HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. all: 55467 / Num. obs: 55301 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.41
Reflection shellResolution: 2.48→2.57 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 3.88 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data processing
HKL-2000data scaling
MOLREPmodel building
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XSO

4xso


Resolution: 2.48→47.4 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.32 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26697 2775 5 %RANDOM
Rwork0.22327 ---
obs0.22546 52491 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.497 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å2-1.17 Å2-0 Å2
2---1.17 Å2-0 Å2
3---3.79 Å2
Refinement stepCycle: LAST / Resolution: 2.48→47.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5618 0 125 219 5962
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195871
X-RAY DIFFRACTIONr_bond_other_d0.0020.025685
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9827990
X-RAY DIFFRACTIONr_angle_other_deg0.838313029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8585731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44524.72250
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30415946
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2871528
X-RAY DIFFRACTIONr_chiral_restr0.0920.2944
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216599
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021325
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_it4.1745.8032936
X-RAY DIFFRACTIONr_mcbond_other4.1735.8022935
X-RAY DIFFRACTIONr_mcangle_it6.2658.6943663
X-RAY DIFFRACTIONr_mcangle_other6.2658.6963664
X-RAY DIFFRACTIONr_scbond_it4.1446.3372935
X-RAY DIFFRACTIONr_scbond_other4.1426.3372935
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5959.324328
X-RAY DIFFRACTIONr_long_range_B_refined10.33146.8036655
X-RAY DIFFRACTIONr_long_range_B_other10.33146.8036656
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.48→2.544 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.416 214 -
Rwork0.355 3806 -
obs--99.85 %

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