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- PDB-6h0p: The structure of C100A mutant of Arabidopsis thaliana UDP-apiose/... -

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Basic information

Entry
Database: PDB / ID: 6h0p
TitleThe structure of C100A mutant of Arabidopsis thaliana UDP-apiose/UDP-xylose synthase in complex with NADH and UDP-D-glucuronic acid
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 / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-D-apiose/UDP-D-xylose synthase 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.47 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
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: 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)89,8016
Polymers87,3132
Non-polymers2,4874
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.564, 144.564, 130.519
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A1 - 9999
2111B1 - 9999

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.784118, 0.620577, -0.006592), (0.620578, 0.784142, 0.002144), (0.006499, -0.002409, -0.999976)50.9014, -17.76119, -32.48728

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Components

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


Mass: 43656.684 Da / Num. of mol.: 2 / Mutation: C100A
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-UGA / URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID / UDP-GLUCURONIC ACID


Mass: 580.285 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N2O18P2

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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: 4.51 Å3/Da / Density % sol: 72.72 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.5
Details: 0.8 M sodium phosphate, 0.8 M potassium phosphate, and 0.1 M sodium-HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 3.47→48.44 Å / Num. obs: 20833 / % possible obs: 99.8 % / Redundancy: 8.3 % / CC1/2: 0.998 / Rmerge(I) obs: 0.151 / Net I/σ(I): 13.1
Reflection shellResolution: 3.47→3.8 Å / Redundancy: 7.9 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4867 / CC1/2: 0.844 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6H0N

6h0n


Resolution: 3.47→48.44 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 63.427 / SU ML: 0.409 / Cross valid method: THROUGHOUT / ESU R Free: 0.46 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23904 1073 5.2 %RANDOM
Rwork0.19589 ---
obs0.19806 19736 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 124.459 Å2
Baniso -1Baniso -2Baniso -3
1-3.36 Å21.68 Å20 Å2
2--3.36 Å2-0 Å2
3----10.89 Å2
Refinement stepCycle: 1 / Resolution: 3.47→48.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5725 0 144 0 5869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0146011
X-RAY DIFFRACTIONr_bond_other_d0.0030.0175253
X-RAY DIFFRACTIONr_angle_refined_deg2.231.6898222
X-RAY DIFFRACTIONr_angle_other_deg1.3721.64912281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1315739
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.34622.712295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10115921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.661533
X-RAY DIFFRACTIONr_chiral_restr0.1130.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026701
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021089
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_it7.02412.0832965
X-RAY DIFFRACTIONr_mcbond_other7.02312.0832964
X-RAY DIFFRACTIONr_mcangle_it10.59718.1453701
X-RAY DIFFRACTIONr_mcangle_other10.59618.1463702
X-RAY DIFFRACTIONr_scbond_it7.50112.3943046
X-RAY DIFFRACTIONr_scbond_other7.512.3943046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.26618.4494522
X-RAY DIFFRACTIONr_long_range_B_refined14.05213415
X-RAY DIFFRACTIONr_long_range_B_other14.02813412
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 5402 / Type: tight thermal / Rms dev position: 10.16 Å / Weight position: 0.5
LS refinement shellResolution: 3.468→3.558 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 82 -
Rwork0.36 1413 -
obs--98.88 %
Refinement TLS params.

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)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21990.23530.00460.2702-0.07080.55190.04870.00860.11790.07180.02470.1379-0.04490.0079-0.07330.07170.00770.03710.04690.00440.074113.0204-60.58852.1954
20.1830.10060.02510.38430.25020.7521-0.05770.15480.1293-0.03660.10310.0499-0.1024-0.0452-0.04540.0302-0.0336-0.0310.14390.11430.09623.5703-57.5468-34.2056
300000000000000-00.0635000.063500.0635000
400000000000000-00.0635000.063500.0635000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 800
2X-RAY DIFFRACTION2B8 - 800

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