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- PDB-3vps: Structure of a novel NAD dependent-NDP-hexosamine 5,6-dehydratase... -

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Basic information

Entry
Database: PDB / ID: 3vps
TitleStructure of a novel NAD dependent-NDP-hexosamine 5,6-dehydratase, TunA, involved in tunicamycin biosynthesis
ComponentsNAD-dependent epimerase/dehydratase
KeywordsTRANSFERASE / tunicamycins / biosynthesis / exo-glycal / dehydratase / Rossmann Fold
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-DIPHOSPHATE-N-ACETYLGLUCOSAMINE / NAD-dependent epimerase/dehydratase
Similarity search - Component
Biological speciesStreptomyces chartreusis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWyszynski, F.J. / Lee, S.S. / Yabe, T. / Wang, H. / Gomez-Escribano, J.P. / Bibb, M.J. / Lee, S.J. / Davies, G.J. / Davis, B.G.
CitationJournal: To be published
Title: Biosynthesis of nucleoside antibiotic tunicamycin proceeds via unique exo-glycal intermediates
Authors: Wyszynski, F.J. / Lee, S.S. / Yabe, T. / Wang, H. / Gomez-Escribano, J.P. / Bibb, M.J. / Lee, S.J. / Davies, G.J. / Davis, B.G.
History
DepositionMar 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: NAD-dependent epimerase/dehydratase
B: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,9076
Polymers70,3662
Non-polymers2,5424
Water3,945219
1
A: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4543
Polymers35,1831
Non-polymers1,2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NAD-dependent epimerase/dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4543
Polymers35,1831
Non-polymers1,2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.453, 51.061, 67.804
Angle α, β, γ (deg.)98.13, 106.65, 94.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein NAD-dependent epimerase/dehydratase / TunA


Mass: 35182.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces chartreusis (bacteria) / Strain: NLLR 3882
References: UniProt: E5KJ94, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical ChemComp-UD1 / URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 607.354 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H27N3O17P2
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 20% polyethylene glycol 3350, 100mM 8v/v tascimate, pH 6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT
DetectorType: RIGAKU SATURN 944+ / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→22.26 Å / Num. all: 42667 / Num. obs: 42667 / Redundancy: 3.7 % / Rmerge(I) obs: 0.18782 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→1.949 Å / Mean I/σ(I) obs: 1.4 / % possible all: 98.55

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→22.26 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.434 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23522 2283 5.1 %RANDOM
Rwork0.18553 ---
obs0.18812 42667 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.811 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20.28 Å2-0.26 Å2
2--0.08 Å20.68 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→22.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 166 219 5003
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0224887
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0022.0276682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.75623.462208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10415767
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0791546
X-RAY DIFFRACTIONr_chiral_restr0.1280.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0223678
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1271.53011
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.53724877
X-RAY DIFFRACTIONr_scbond_it4.01431876
X-RAY DIFFRACTIONr_scangle_it6.2784.51805
X-RAY DIFFRACTIONr_rigid_bond_restr2.30234887
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 175 -
Rwork0.208 3092 -
obs--98.55 %
Refinement TLS params.

T13: 0.0088 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0006-0.0012-0.00160.00240.00320.00440.00060.00010.0003-0.00080.0003-0.0006-0.00070.0001-0.00090.0159-0.00370.0259-0.02230.0257-21.0385-5.1583-2.2697
20.0036-0.00220.01330.0014-0.00840.04950.0013-0.00070.0001-0.00130.00040.00020.0062-0.0007-0.00170.0162-0.00460.0285-0.02180.0275-34.9369-11.5418-35.5177
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 309
2X-RAY DIFFRACTION1A400 - 401
3X-RAY DIFFRACTION2B8 - 310
4X-RAY DIFFRACTION2B400 - 401

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