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- PDB-4tqg: Crystal structure of Megavirus UDP-GlcNAc 4,6-dehydratase, 5-epim... -

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Basic information

Entry
Database: PDB / ID: 4tqg
TitleCrystal structure of Megavirus UDP-GlcNAc 4,6-dehydratase, 5-epimerase Mg534
ComponentsPutative dTDP-d-glucose 4 6-dehydratase
KeywordsSUGAR BINDING PROTEIN / NADP binding Sugar pathway
Function / homology
Function and homology information


Polysaccharide biosynthesis protein, CapD-like domain / Polysaccharide biosynthesis protein / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / Putative dTDP-d-glucose 4 6-dehydratase
Similarity search - Component
Biological speciesMegavirus chiliensis
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsJeudy, S. / Piacente, F. / De Castro, C. / Molinaro, A. / Salis, A. / Damonte, G. / Bernardi, C. / Tonetti, M. / Claverie, J.M. / Abergel, C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Giant Virus Megavirus chilensis Encodes the Biosynthetic Pathway for Uncommon Acetamido Sugars.
Authors: Piacente, F. / De Castro, C. / Jeudy, S. / Molinaro, A. / Salis, A. / Damonte, G. / Bernardi, C. / Abergel, C. / Tonetti, M.G.
History
DepositionJun 11, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 2.0Mar 11, 2020Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / pdbx_struct_special_symmetry / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_special_symmetry.auth_seq_id / _struct_site_gen.auth_seq_id
Revision 2.1Dec 20, 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: Putative dTDP-d-glucose 4 6-dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6852
Polymers36,9391
Non-polymers7451
Water1,71195
1
A: Putative dTDP-d-glucose 4 6-dehydratase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)226,10912
Polymers221,6366
Non-polymers4,4736
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
crystal symmetry operation10_665-y+1,-x+1,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area25790 Å2
ΔGint-45 kcal/mol
Surface area66200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.509, 153.509, 60.680
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-587-

HOH

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Components

#1: Protein Putative dTDP-d-glucose 4 6-dehydratase


Mass: 36939.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Megavirus chiliensis / Gene: mg534 / Production host: Escherichia coli (E. coli) / References: UniProt: G5CSR9
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.79 Å3/Da / Density % sol: 55.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: malic acid 0.1M, PEG 3350 22-25% (w/v) / PH range: 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 4, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.2→38.377 Å / Num. all: 21901 / Num. obs: 21901 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.01 Å2 / Rpim(I) all: 0.036 / Rrim(I) all: 0.094 / Rsym value: 0.087 / Net I/av σ(I): 7.111 / Net I/σ(I): 15.5 / Num. measured all: 150564
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.2-2.326.40.2992.61993131320.1270.2996100
2.32-2.466.90.243.32041129590.0980.247.6100
2.46-2.6370.1834.31965427890.0740.1839.8100
2.63-2.847.10.1385.61858926340.0560.13812.1100
2.84-3.117.10.0938.21705024100.0370.09315.8100
3.11-3.487.10.06311.71554621960.0250.06320.8100
3.48-4.0270.0669.41381619620.0270.06624.9100
4.02-4.926.90.0669.11163116770.0260.06628100
4.92-6.966.70.05410.8905113460.0220.05426.6100
6.96-38.3776.10.02424.448857960.0110.02428.599.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.2 Å38.38 Å
Translation2.2 Å38.38 Å

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALA3.3.20data scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4J2O

4j2o


Resolution: 2.2→38.377 Å / FOM work R set: 0.8655 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 1119 5.11 %Random selection
Rwork0.1934 20771 --
obs0.1954 21890 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.12 Å2 / Biso mean: 21.38 Å2 / Biso min: 4.1 Å2
Refinement stepCycle: final / Resolution: 2.2→38.377 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 48 95 2523
Biso mean--28.02 18.36 -
Num. residues----297
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072493
X-RAY DIFFRACTIONf_angle_d1.1563370
X-RAY DIFFRACTIONf_chiral_restr0.089388
X-RAY DIFFRACTIONf_plane_restr0.004417
X-RAY DIFFRACTIONf_dihedral_angle_d19.081960
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2002-2.30030.27671470.201825322679
2.3003-2.42160.28161240.201725492673
2.4216-2.57330.23611530.205725382691
2.5733-2.77190.24641220.204625692691
2.7719-3.05070.2381370.2125842721
3.0507-3.49190.24641660.195525572723
3.4919-4.39840.17191320.174926452777
4.3984-38.38310.2411380.18627972935

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