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- PDB-2gn4: Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in comp... -

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Basic information

Entry
Database: PDB / ID: 2gn4
TitleCrystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADPH and UDP-GlcNAc
ComponentsUDP-GlcNAc C6 dehydratase
KeywordsLYASE / Rossmann fold / TYK triad / SDR / enzyme / dehydratase / UDP-GlcNAc / NADP / NADPH
Function / homology
Function and homology information


UDP-N-acetylglucosamine 4,6-dehydratase (configuration-inverting) / lyase activity / nucleotide binding
Similarity search - Function
UDP-N-acetylglucosamine 4,6-dehydratase (inverting) / Polysaccharide biosynthesis protein, CapD-like domain / : / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold ...UDP-N-acetylglucosamine 4,6-dehydratase (inverting) / Polysaccharide biosynthesis protein, CapD-like domain / : / Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / UDP-galactose 4-epimerase; domain 1 / 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
Chem-NDP / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsIshiyama, N. / Creuzenet, C. / Lam, J.S. / Berghuis, A.M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural Studies of FlaA1 from Helicobacter pylori Reveal the Mechanism for Inverting 4,6-Dehydratase Activity.
Authors: Ishiyama, N. / Creuzenet, C. / Miller, W.L. / Demendi, M. / Anderson, E.M. / Harauz, G. / Lam, J.S. / Berghuis, A.M.
History
DepositionApr 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,5458
Polymers77,4492
Non-polymers3,0966
Water5,549308
1
A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules

A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules

A: UDP-GlcNAc C6 dehydratase
B: UDP-GlcNAc C6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,63624
Polymers232,3486
Non-polymers9,28818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)111.357, 111.357, 107.991
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe biological assembly is a hexamer generated from the two protomers in the asymmetric unit by the operations:(-Y,X-Y,Z) and (-X+Y,-X,Z)

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Components

#1: Protein UDP-GlcNAc C6 dehydratase / flaA1 protein


Mass: 38724.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: HP0840 / Plasmid: pET23 derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: O25511, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 10% (v/v) PEG-200, 100 mM MES, 5% (v/w) PEG-3000, 4% (v/v) acetone, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 31, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 57284 / % possible obs: 95.7 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.049 / Χ2: 1.004 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.97 Å / % possible obs: 87.5 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.422 / Num. unique obs: 5267 / Χ2: 0.93

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
ADSCdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1sb8

1sb8


Resolution: 1.9→50 Å / FOM work R set: 0.846 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 5824 9.7 %random
Rwork0.197 ---
obs-57284 95.7 %-
Solvent computationBsol: 55.428 Å2
Displacement parametersBiso mean: 39.283 Å2
Baniso -1Baniso -2Baniso -3
1--3.97 Å2-4.05 Å20 Å2
2---3.97 Å20 Å2
3---7.939 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5213 0 198 308 5719
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.6871.5
X-RAY DIFFRACTIONc_scbond_it2.6132
X-RAY DIFFRACTIONc_mcangle_it2.5062
X-RAY DIFFRACTIONc_scangle_it3.6572.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.910.411900.306846936
1.91-1.930.32870.285847934
1.93-1.940.329920.278874966
1.94-1.950.316950.285877972
1.95-1.970.281880.269121000
1.97-1.980.2811080.2659461054
1.98-20.2641110.2499801091
2-2.010.271130.24610131126
2.01-2.030.2761360.2399711107
2.03-2.050.2831190.2229701089
2.05-2.060.2411130.23310511164
2.06-2.080.2551180.2299361054
2.08-2.10.2621220.21710441166
2.1-2.120.2621030.20910041107
2.12-2.140.2651150.21210331148
2.14-2.160.2391170.22810241141
2.16-2.180.2611240.2210391163
2.18-2.20.2221130.19510041117
2.2-2.230.2291210.19210501171
2.23-2.250.2551280.20510411169
2.25-2.280.2551220.19910351157
2.28-2.310.251230.210191142
2.31-2.330.2141010.19910531154
2.33-2.360.2191220.18910491171
2.36-2.390.2421310.20110371168
2.39-2.430.2591140.19510791193
2.43-2.460.2391250.19110441169
2.46-2.50.2251000.19510691169
2.5-2.540.2231090.19610881197
2.54-2.580.2891170.21110561173
2.58-2.620.2341050.20410661171
2.62-2.670.2751130.20910871200
2.67-2.720.2381450.18910691214
2.72-2.780.2641200.210501170
2.78-2.840.2281210.18910711192
2.84-2.90.2491400.18810571197
2.9-2.980.2271280.1910651193
2.98-3.060.1881180.17510741192
3.06-3.150.2161190.19910781197
3.15-3.250.1991100.19110851195
3.25-3.370.2261340.18810621196
3.37-3.50.2261280.19410641192
3.5-3.660.2311260.19210611187
3.66-3.850.2061260.17610941220
3.85-4.090.2031130.17710801193
4.09-4.410.171130.1710761189
4.41-4.850.1751120.14910901202
4.85-5.560.1991420.18410691211
5.56-70.281090.23211001209
7-500.010.221250.20810711196
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2ndp_ni.par
X-RAY DIFFRACTION3ud1_ni.par
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5mes_ni.par

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