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- PDB-6kvc: MoeE5 in complex with UDP-glucose and NAD -

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Basic information

Entry
Database: PDB / ID: 6kvc
TitleMoeE5 in complex with UDP-glucose 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-GLUCOSE / MoeE5
Similarity search - Component
Biological speciesStreptomyces viridosporus ATCC 14672 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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 4, 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

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Assembly

Deposited unit
A: MoeE5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7743
Polymers36,5441
Non-polymers1,2302
Water7,098394
1
A: MoeE5
hetero molecules

A: MoeE5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,5486
Polymers73,0882
Non-polymers2,4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7150 Å2
ΔGint-47 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.047, 59.047, 197.975
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-881-

HOH

21A-894-

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 / 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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER / Uridine diphosphate glucose


Mass: 566.302 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H24N2O17P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.36 Å3/Da / Density % sol: 47.9 %
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: Apr 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.66→25 Å / Num. obs: 42601 / % possible obs: 99.8 % / Redundancy: 10.9 % / Biso Wilson estimate: 22.06 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 24.5
Reflection shellResolution: 1.66→1.72 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 4165 / % possible all: 99.8

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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: 1.66→24.75 Å / SU ML: 0.1382 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.5802
RfactorNum. reflection% reflection
Rfree0.191 1996 4.7 %
Rwork0.1549 --
obs0.1565 42426 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.46 Å2
Refinement stepCycle: LAST / Resolution: 1.66→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2244 0 80 394 2718
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01642405
X-RAY DIFFRACTIONf_angle_d1.4923275
X-RAY DIFFRACTIONf_chiral_restr0.0995387
X-RAY DIFFRACTIONf_plane_restr0.0095416
X-RAY DIFFRACTIONf_dihedral_angle_d17.31461415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.70.25751400.20612841X-RAY DIFFRACTION99.8
1.7-1.750.22621400.18212831X-RAY DIFFRACTION99.97
1.75-1.80.21021390.16832834X-RAY DIFFRACTION100
1.8-1.860.19631420.16882860X-RAY DIFFRACTION99.7
1.86-1.920.19451390.1632817X-RAY DIFFRACTION99.66
1.92-20.18671430.15962861X-RAY DIFFRACTION99.67
2-2.090.21681410.16042862X-RAY DIFFRACTION99.73
2.09-2.20.17761400.1562862X-RAY DIFFRACTION99.6
2.2-2.340.20741400.16152828X-RAY DIFFRACTION99
2.34-2.520.21211420.15892865X-RAY DIFFRACTION99.4
2.52-2.770.17631430.16062903X-RAY DIFFRACTION99.44
2.77-3.170.17331450.1592932X-RAY DIFFRACTION99.61
3.17-3.990.17461470.14132980X-RAY DIFFRACTION99.71
3.99-24.750.19411550.14573154X-RAY DIFFRACTION99.58

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