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- PDB-2gn9: Crystal structure of UDP-GlcNAc inverting 4,6-dehydratase in comp... -

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Basic information

Entry
Database: PDB / ID: 2gn9
TitleCrystal structure of UDP-GlcNAc inverting 4,6-dehydratase in complex with NADP and UDP-Glc
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-GLUCOSE / UDP-N-acetylglucosamine 4,6-dehydratase (inverting)
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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)80,2647
Polymers77,4492
Non-polymers2,8155
Water1,36976
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)240,79221
Polymers232,3486
Non-polymers8,44415
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
MethodPQS
2
B: UDP-GlcNAc C6 dehydratase
hetero molecules

A: UDP-GlcNAc C6 dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,2647
Polymers77,4492
Non-polymers2,8155
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area8000 Å2
ΔGint-40 kcal/mol
Surface area25800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.376, 112.376, 107.349
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-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER


Mass: 566.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H24N2O17P2
#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.: 76 / 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: 2.53 Å3/Da / Density % sol: 51.29 %
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: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 18312 / % possible obs: 99.6 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.083 / Χ2: 0.989 / Net I/σ(I): 8.7
Reflection shellResolution: 2.8→2.9 Å / % possible obs: 99.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.259 / Num. unique obs: 1849 / Χ2: 0.937

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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: 2.8→50 Å / FOM work R set: 0.76 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1802 9.5 %random
Rwork0.22 ---
obs-18312 96.1 %-
Solvent computationBsol: 54.111 Å2
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1--11.551 Å2-17.56 Å20 Å2
2---11.551 Å20 Å2
3---23.102 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5163 0 180 76 5419
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it3.4711.5
X-RAY DIFFRACTIONc_scbond_it5.4222
X-RAY DIFFRACTIONc_mcangle_it5.3252
X-RAY DIFFRACTIONc_scangle_it7.1042.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 36

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
2.8-2.830.378390.306322361
2.83-2.850.317500.264406456
2.85-2.880.385470.272452499
2.88-2.910.386530.275418471
2.91-2.940.334400.293461501
2.94-2.980.418470.271470517
2.98-3.010.319490.263450499
3.01-3.040.444460.275482528
3.04-3.080.331530.279437490
3.08-3.120.433430.246458501
3.12-3.160.304620.255461523
3.16-3.210.394500.29450500
3.21-3.250.394520.244473525
3.25-3.30.272450.173490535
3.3-3.350.304560.201448504
3.35-3.410.348540.234470524
3.41-3.460.331420.231488530
3.46-3.530.272430.215486529
3.53-3.60.285480.221456504
3.6-3.670.254530.193476529
3.67-3.750.341550.209457512
3.75-3.840.237510.18470521
3.84-3.930.216530.149461514
3.93-4.040.317420.168490532
4.04-4.160.264690.18456525
4.16-4.290.175490.137469518
4.29-4.440.328460.182487533
4.44-4.620.227450.169473518
4.62-4.830.23510.17478529
4.83-5.090.21540.163474528
5.09-5.410.245560.183474530
5.41-5.820.224540.188471525
5.82-6.410.359640.219458522
6.41-7.340.312520.201492544
7.34-9.250.228400.206502542
9.25-500.010.913490.651344393
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2nap_ni.par
X-RAY DIFFRACTION3upg_ni.par
X-RAY DIFFRACTION4mes_ni.par
X-RAY DIFFRACTION5CNS_TOPPAR:water_rep.param

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