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- PDB-6kv9: MoeE5 in complex with UDP-glucuronic acid and NAD -

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Basic information

Entry
Database: PDB / ID: 6kv9
TitleMoeE5 in complex with UDP-glucuronic acid and NAD
ComponentsMoeE5
KeywordsBIOSYNTHETIC PROTEIN / substrate / complex / antibiotic / epimerase / galacturonic acid
Function / homology
Function and homology information


: / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / MoeE5
Similarity search - Component
Biological speciesStreptomyces viridosporus ATCC 14672 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsKo, T.-P. / Liu, W. / Sun, H. / Liu, W. / Chen, C.-C. / Guo, R.-T.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structure of an antibiotic-synthesizing UDP-glucuronate 4-epimerase MoeE5 in complex with substrate.
Authors: Sun, H. / Ko, T.P. / Liu, W. / Liu, W. / Zheng, Y. / Chen, C.C. / Guo, R.T.
History
DepositionSep 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.2Nov 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MoeE5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7883
Polymers36,5441
Non-polymers1,2442
Water6,990388
1
A: MoeE5
hetero molecules

A: MoeE5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5766
Polymers73,0882
Non-polymers2,4874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area6910 Å2
ΔGint-50 kcal/mol
Surface area22680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.159, 59.159, 200.387
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-977-

HOH

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Components

#1: Protein MoeE5


Mass: 36544.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridosporus ATCC 14672 (bacteria)
Gene: moeE5
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A003
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N2O18P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 53.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: Na-citrate, Bis-Tris propane, PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→25 Å / Num. obs: 60430 / % possible obs: 99.5 % / Redundancy: 10.7 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 57.2
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 5731 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb 4zrn

4zrn


Resolution: 1.48→23.8 Å / SU ML: 0.1368 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.5093
RfactorNum. reflection% reflection
Rfree0.1861 2000 3.32 %
Rwork0.1592 --
obs0.16 60321 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 23.16 Å2
Refinement stepCycle: LAST / Resolution: 1.48→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 388 2715
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01622439
X-RAY DIFFRACTIONf_angle_d1.53783324
X-RAY DIFFRACTIONf_chiral_restr0.112390
X-RAY DIFFRACTIONf_plane_restr0.0098426
X-RAY DIFFRACTIONf_dihedral_angle_d23.4674892
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.48-1.520.25481360.22343951X-RAY DIFFRACTION95.65
1.52-1.560.24311380.20064056X-RAY DIFFRACTION98.66
1.56-1.60.25791410.18164093X-RAY DIFFRACTION99.95
1.6-1.650.19281410.1774090X-RAY DIFFRACTION99.98
1.65-1.710.20551410.17344131X-RAY DIFFRACTION100
1.71-1.780.18291420.16234131X-RAY DIFFRACTION99.98
1.78-1.860.20011410.16584150X-RAY DIFFRACTION99.98
1.86-1.960.1921420.15694125X-RAY DIFFRACTION100
1.96-2.080.18511420.164157X-RAY DIFFRACTION99.98
2.08-2.250.18861450.1614197X-RAY DIFFRACTION100
2.25-2.470.16191450.15734216X-RAY DIFFRACTION100
2.47-2.830.18941440.16024231X-RAY DIFFRACTION99.98
2.83-3.560.19771480.14784281X-RAY DIFFRACTION99.98
3.56-23.80.16341540.15064512X-RAY DIFFRACTION99.15

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