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- PDB-4qqr: Structural insight into nucleotide rhamnose synthase/epimerase-re... -

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Basic information

Entry
Database: PDB / ID: 4qqr
TitleStructural insight into nucleotide rhamnose synthase/epimerase-reductase from Arabidopsis thaliana
Components3,5-epimerase/4-reductase
KeywordsOXIDOREDUCTASE / BETA BARREL / Rossmann Fold / epimerase-reductase
Function / homology
Function and homology information


UDP-rhamnose biosynthetic process / UDP-4-keto-6-deoxy-glucose-3,5-epimerase activity / UDP-4-keto-rhamnose-4-keto-reductase activity / dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / plasmodesma / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor ...UDP-rhamnose biosynthetic process / UDP-4-keto-6-deoxy-glucose-3,5-epimerase activity / UDP-4-keto-rhamnose-4-keto-reductase activity / dTDP-4-dehydrorhamnose reductase / dTDP-4-dehydrorhamnose reductase activity / dTDP-4-dehydrorhamnose 3,5-epimerase / dTDP-4-dehydrorhamnose 3,5-epimerase activity / dTDP-rhamnose biosynthetic process / plasmodesma / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / cell wall organization / oxidoreductase activity / plasma membrane / cytosol
Similarity search - Function
RmlD-like substrate binding domain / RmlD substrate binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional dTDP-4-dehydrorhamnose 3,5-epimerase/dTDP-4-dehydrorhamnose reductase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsHan, X. / Liu, X.
CitationJournal: To be Published
Title: Structural insight into nucleotide rhamnose synthase/epimerase-reductase from Arabidopsis thaliana
Authors: Han, X. / Liu, X.
History
DepositionJun 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2015Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: 3,5-epimerase/4-reductase
B: 3,5-epimerase/4-reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,89312
Polymers67,2692
Non-polymers62510
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-242 kcal/mol
Surface area23050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.589, 61.943, 176.774
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3,5-epimerase/4-reductase / F16P17.17 protein / Putative uncharacterized protein At1g63000 / UDP-4-keto-6-deoxy-d-glucose-3 / 5- ...F16P17.17 protein / Putative uncharacterized protein At1g63000 / UDP-4-keto-6-deoxy-d-glucose-3 / 5-epimerase-4-reductase 1


Mass: 33634.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g63000, ER, F16P17.17, NRS, NRS/ER / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LQ04
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.59 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.8M ammonium sulfate, 0.1mM ZnCl2, 1mM DTT and 0.1M Hepes pH 6.5. , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1.2826 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Nov 15, 2012
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2826 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34737 / % possible obs: 95 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.7-4.131100
4.13-7.051100
7.05-501100

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.7→41.779 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 27.68 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 3485 10.03 %RANDOM
Rwork0.1985 ---
all0.247 ---
obs0.2051 34735 94.42 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.022 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.3851 Å20 Å2-0 Å2
2--6.5156 Å2-0 Å2
3----7.9008 Å2
Refinement stepCycle: LAST / Resolution: 2.7→41.779 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4270 0 14 68 4352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094358
X-RAY DIFFRACTIONf_angle_d1.1795899
X-RAY DIFFRACTIONf_dihedral_angle_d15.961599
X-RAY DIFFRACTIONf_chiral_restr0.078668
X-RAY DIFFRACTIONf_plane_restr0.007748
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.603-2.63860.40121310.2668116889
2.6386-2.67630.36531370.2711122092
2.6763-2.71630.34271470.2531128395
2.7163-2.75870.3511470.2645125998
2.7587-2.80390.35311540.25971347100
2.8039-2.85230.30411420.25451309100
2.8523-2.90410.35671500.24161316100
2.9041-2.960.34041510.24751340100
2.96-3.02040.33331430.23961308100
3.0204-3.0860.33191540.24681360100
3.086-3.15780.32621420.21541294100
3.1578-3.23670.32011470.23091336100
3.2367-3.32420.24951500.19451332100
3.3242-3.4220.31671470.20631308100
3.422-3.53240.31031470.20481329100
3.5324-3.65860.3955950.200286395
3.6586-3.80490.2298770.23172994
3.8049-3.9780.25141440.206124195
3.978-4.18750.25881400.1681129298
4.1875-4.44960.19281420.1489130997
4.4496-4.79270.16981440.1351127097
4.7927-5.27420.20091430.1569130599
5.2742-6.03540.24061420.176131899
6.0354-7.59650.23931440.1903130198
7.5965-41.78470.21511250.2068111584

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