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- PDB-2gn8: Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in comp... -

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Basic information

Entry
Database: PDB / ID: 2gn8
TitleCrystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADP and UDP
ComponentsUDP-GlcNAc C6 dehydratase
KeywordsLYASE / Rossmann fold / TYK triad / SDR / enzyme / dehydratase / UDP-GlcNAc / NADP
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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: Derived calculations / 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)79,9407
Polymers77,4492
Non-polymers2,4905
Water5,188288
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)239,81921
Polymers232,3486
Non-polymers7,47115
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7350 Å2
ΔGint-38 kcal/mol
Surface area26490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.056, 111.056, 107.790
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#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-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
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 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43145 / % possible obs: 97.9 % / Redundancy: 8.5 % / Rmerge(I) obs: 0.069 / Χ2: 1.001 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.18 Å / % possible obs: 99.8 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.409 / Num. unique obs: 4389 / Χ2: 1.044

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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: 2.1→50 Å / FOM work R set: 0.849 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.245 4309 9.8 %random
Rwork0.209 ---
obs-43145 97.9 %-
Solvent computationBsol: 55.69 Å2
Displacement parametersBiso mean: 40.183 Å2
Baniso -1Baniso -2Baniso -3
1--1.722 Å2-1.829 Å20 Å2
2---1.722 Å20 Å2
3---3.444 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.14 Å
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 158 288 5609
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3871.5
X-RAY DIFFRACTIONc_scbond_it2.0192
X-RAY DIFFRACTIONc_mcangle_it2.2462
X-RAY DIFFRACTIONc_scangle_it2.8882.5
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
2.1-2.110.289900.254707797
2.11-2.130.243960.242732828
2.13-2.140.251830.242735818
2.14-2.160.283840.236731815
2.16-2.180.266820.238753835
2.18-2.190.277910.224733824
2.19-2.210.249890.231790879
2.21-2.230.229590.206767826
2.23-2.240.239830.221765848
2.24-2.260.236790.198759838
2.26-2.280.233850.221757842
2.28-2.30.238890.221754843
2.3-2.320.281770.215773850
2.32-2.340.256970.213758855
2.34-2.370.252760.204770846
2.37-2.390.28840.2760844
2.39-2.410.265920.211773865
2.41-2.440.263920.195732824
2.44-2.460.257850.201811896
2.46-2.490.218880.189759847
2.49-2.520.234900.203756846
2.52-2.550.268880.201786874
2.55-2.580.258830.235791874
2.58-2.610.258900.209772862
2.61-2.650.272830.218783866
2.65-2.680.226930.214770863
2.68-2.720.218820.208801883
2.72-2.760.272710.22798869
2.76-2.80.276900.229792882
2.8-2.850.301930.223774867
2.85-2.90.256760.207797873
2.9-2.950.247910.198773864
2.95-3.010.241050.203789894
3.01-3.070.238770.225794871
3.07-3.140.235750.231790865
3.14-3.210.263930.223784877
3.21-3.290.2531000.22799899
3.29-3.380.243870.203792879
3.38-3.480.2481030.208774877
3.48-3.590.197820.198802884
3.59-3.720.22910.19783874
3.72-3.870.204760.178819895
3.87-4.040.249870.189788875
4.04-4.260.202810.188808889
4.26-4.520.225800.175793873
4.52-4.870.256810.178815896
4.87-5.360.234940.218796890
5.36-6.140.284890.257808897
6.14-7.740.26860.222802888
7.74-500.010.243910.216788879
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2nap_ni.par
X-RAY DIFFRACTION3udp_ni.par
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION5mes_ni.par

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