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- PDB-6h0n: The structure of wild-type Arabidopsis thaliana UDP-apiose/UDP-xy... -

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Basic information

Entry
Database: PDB / ID: 6h0n
TitleThe structure of wild-type Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NAD+ and UDP
ComponentsUDP-D-apiose/UDP-D-xylose synthase 1
KeywordsOXIDOREDUCTASE / Enzyme catalysis / glycobiology / short-chain dehydrogenases/reductases (SDR) / aldol cleavage / substrate-assisted reaction
Function / homology
Function and homology information


nucleotide-sugar biosynthetic process / UDP-glucuronate decarboxylase activity / cell wall organization / peroxisome / NAD binding / cytoplasm / cytosol
Similarity search - Function
Bifunctional polymyxin resistance protein ArnA-like, extended (e) SDRs / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / URIDINE-5'-DIPHOSPHATE / UDP-D-apiose/UDP-D-xylose synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsSavino, S. / Mattevi, A.
CitationJournal: Nat Catal / Year: 2019
Title: Deciphering the enzymatic mechanism of sugar ring contraction in UDP-apiose biosynthesis.
Authors: Savino, S. / Borg, A.J.E. / Dennig, A. / Pfeiffer, M. / de Giorgi, F. / Weber, H. / Dubey, K.D. / Rovira, C. / Mattevi, A. / Nidetzky, B.
History
DepositionJul 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 17, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-D-apiose/UDP-D-xylose synthase 1
B: UDP-D-apiose/UDP-D-xylose synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,7038
Polymers87,3782
Non-polymers2,3256
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8170 Å2
ΔGint-77 kcal/mol
Surface area27480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.028, 146.028, 132.845
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 8 - 384 / Label seq-ID: 8 - 384

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein UDP-D-apiose/UDP-D-xylose synthase 1


Mass: 43688.750 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AXS1, At2g27860, F15K20.4 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZUY6
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 4.79 Å3/Da / Density % sol: 74.3 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5
Details: 0.8 M sodium phosphate, 0.8 M potassium phosphate, 0.1 M sodium-HEPES

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00368 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00368 Å / Relative weight: 1
ReflectionResolution: 3.02→126.46 Å / Num. obs: 32264 / % possible obs: 98.9 % / Redundancy: 4.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.146 / Net I/σ(I): 9.2
Reflection shellResolution: 3.02→3.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / Num. unique obs: 4488 / CC1/2: 0.378 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SLG

3slg


Resolution: 3.02→126.46 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.584 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R: 0.611 / ESU R Free: 0.345 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25278 1640 5.1 %RANDOM
Rwork0.20711 ---
obs0.20944 30595 98.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.855 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20.77 Å20 Å2
2--1.54 Å2-0 Å2
3----5.01 Å2
Refinement stepCycle: 1 / Resolution: 3.02→126.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5840 0 148 23 6011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196124
X-RAY DIFFRACTIONr_bond_other_d0.0020.025553
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9948354
X-RAY DIFFRACTIONr_angle_other_deg1.076312878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3635742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.30924.111270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.06415983
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3811538
X-RAY DIFFRACTIONr_chiral_restr0.0990.2941
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216713
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021227
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_it5.4087.7862983
X-RAY DIFFRACTIONr_mcbond_other5.4077.7852982
X-RAY DIFFRACTIONr_mcangle_it7.93511.6863720
X-RAY DIFFRACTIONr_mcangle_other7.93411.6873721
X-RAY DIFFRACTIONr_scbond_it5.838.1473141
X-RAY DIFFRACTIONr_scbond_other5.838.1483140
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8512.0544635
X-RAY DIFFRACTIONr_long_range_B_refined10.78291.6956847
X-RAY DIFFRACTIONr_long_range_B_other10.78291.6886848
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23974 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.018→3.096 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 133 -
Rwork0.369 2057 -
obs--91.25 %

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