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- PDB-6ypb: NUDIX1 hydrolase from Rosa x hybrida -

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Basic information

Entry
Database: PDB / ID: 6ypb
TitleNUDIX1 hydrolase from Rosa x hybrida
ComponentsGeranyl diphosphate phosphohydrolase
KeywordsHYDROLASE / Nudix hydrolase / rose scent / sesquiterpenes
Function / homology
Function and homology information


geranyl diphosphate phosphohydrolase / hydrolase activity / metal ion binding / cytoplasm
Similarity search - Function
NUDIX hydrolase / NUDIX hydrolase, conserved site / Nudix box signature. / NUDIX domain / Nudix hydrolase domain profile. / NUDIX hydrolase domain / NUDIX hydrolase-like domain superfamily
Similarity search - Domain/homology
Geranyl diphosphate phosphohydrolase
Similarity search - Component
Biological speciesRosa hybrid cultivar (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsDegut, C. / Rety, S. / Tisne, C. / Baudino, S.
CitationJournal: Plant J. / Year: 2020
Title: Functional diversification in the Nudix hydrolase gene family drives sesquiterpene biosynthesis in Rosa × wichurana.
Authors: Sun, P. / Degut, C. / Rety, S. / Caissard, J.C. / Hibrand-Saint Oyant, L. / Bony, A. / Paramita, S.N. / Conart, C. / Magnard, J.L. / Jeauffre, J. / Abd-El-Haliem, A.M. / Marie-Magdelaine, J. ...Authors: Sun, P. / Degut, C. / Rety, S. / Caissard, J.C. / Hibrand-Saint Oyant, L. / Bony, A. / Paramita, S.N. / Conart, C. / Magnard, J.L. / Jeauffre, J. / Abd-El-Haliem, A.M. / Marie-Magdelaine, J. / Thouroude, T. / Baltenweck, R. / Tisne, C. / Foucher, F. / Haring, M. / Hugueney, P. / Schuurink, R.C. / Baudino, S.
History
DepositionApr 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 16, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 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

Downloads & links

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Assembly

Deposited unit
A: Geranyl diphosphate phosphohydrolase


Theoretical massNumber of molelcules
Total (without water)16,8031
Polymers16,8031
Non-polymers00
Water1,40578
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.674, 48.674, 103.132
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-257-

HOH

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Components

#1: Protein Geranyl diphosphate phosphohydrolase / Nudix hydrolase 1 / RhNUDX1


Mass: 16802.867 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rosa hybrid cultivar (plant) / Gene: NUDIX1 / Organ: petals / Production host: Escherichia coli (E. coli)
References: UniProt: M4I1C6, geranyl diphosphate phosphohydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 200 mM ammonium sulfate, 100 mM sodium acetate , 25% PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→39.02 Å / Num. obs: 16180 / % possible obs: 99.78 % / Redundancy: 11.1 % / Biso Wilson estimate: 20.27 Å2 / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.208 / Rpim(I) all: 0.065 / Net I/σ(I): 7.91
Reflection shellResolution: 1.7→1.761 Å / Redundancy: 11.4 % / Rmerge(I) obs: 1.799 / Mean I/σ(I) obs: 0.96 / Num. unique obs: 1581 / CC1/2: 0.464 / CC star: 0.796 / Rpim(I) all: 0.06507 / % possible all: 99.56

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
DIALS1.14.12data reduction
DIALS1.14.12data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KYX

4kyx


Resolution: 1.7→39.02 Å / SU ML: 0.2513 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.0517
RfactorNum. reflection% reflection
Rfree0.2432 1625 10.05 %
Rwork0.2083 --
obs0.2119 16172 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.16 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1043 0 0 78 1121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591087
X-RAY DIFFRACTIONf_angle_d0.83051482
X-RAY DIFFRACTIONf_chiral_restr0.0481160
X-RAY DIFFRACTIONf_plane_restr0.0052195
X-RAY DIFFRACTIONf_dihedral_angle_d17.1544402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.43331330.38711200X-RAY DIFFRACTION99.55
1.75-1.810.34321350.33431170X-RAY DIFFRACTION99.92
1.81-1.870.31951310.24951218X-RAY DIFFRACTION100
1.87-1.950.24661310.22331191X-RAY DIFFRACTION99.92
1.95-2.030.28921300.23471192X-RAY DIFFRACTION100
2.03-2.140.26781340.20981191X-RAY DIFFRACTION99.92
2.14-2.280.19161370.19241201X-RAY DIFFRACTION99.93
2.28-2.450.19491360.18771198X-RAY DIFFRACTION100
2.45-2.70.21441350.1951216X-RAY DIFFRACTION99.78
2.7-3.090.23781360.191219X-RAY DIFFRACTION99.93
3.09-3.890.18151370.18451228X-RAY DIFFRACTION99.27
3.89-39.020.27581500.20111323X-RAY DIFFRACTION99.33
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)
17.859832438293.050319820243.343572836182.361309206561.812286852344.49287437007-0.2844123626390.0312130444362-0.41132813376-0.4193261532840.2137922566340.06587663055550.323752090289-0.0844927282711-0.08966239031940.285001028808-0.0240886460654-0.02280912902450.1374780194620.02999428107550.175599438188-33.869203823712.22800511963.6724198718
23.7951243666-1.611647169010.3141432062454.81964301074-1.401312871957.04115735351-0.08007611175070.0547061122607-0.295677456187-1.1501347611-0.779998728199-0.7201118036781.453862970442.028000326310.04077190308220.273225497520.1989486998020.02311531680060.4678936707320.1340638482410.16762724217-20.192286305710.77272430657.85742139882
32.462759905540.0671373367616-1.406257458861.672317171660.4859064660822.13157311084-0.541307458758-0.174907188155-0.2015552803920.1342796185890.4043624611190.3184479214770.717825118516-0.04695580166170.1238871743120.26031601365-0.0321418213306-0.0176413573110.1577416535020.06635937591570.208758236586-38.66747580111.33160597659.57465952684
44.67513646995-2.214385954992.110458419973.85820589235-2.028721429353.032200633760.0160177859283-0.0848863174483-0.01147915752820.129408171780.001942082896160.03500267885480.01184538313190.041632192127-0.06860736457210.162558028540.028366557663-0.01367859284790.1020006904340.01152869866410.116838952251-31.872673275814.84104719815.8281875867
53.87280100751-0.4309477660130.9881822422771.24414903945-0.928760857014.641123426970.2704679603090.264532630148-0.402868912223-0.1424072322290.00413849129076-0.07370614354830.4396944285570.0438412436477-0.09814719864530.2010274503730.033280493208-0.06501579285530.1110290003670.003165312033670.164208523089-32.836362453815.70412436390.567526093465
61.63189873506-0.9194751101650.795063479883.05946045339-0.9621148564554.366589783420.03768576340990.2302038857350.121230595647-0.0772035718204-0.280426664978-0.2735370160810.2936020945910.8488308054640.1638387572350.141195646450.0634222488043-0.006812199542430.3169839696480.0632663158660.187589111988-19.83737517512.178114588912.7353367956
74.286583742760.1737593329880.2531754517584.7273828360.01514201299485.486444419660.223418489489-0.0511228234736-0.148498732824-0.638917021233-0.515883276605-0.344952169693-0.4510601396970.297773077920.1564035308950.2644968772590.03163547492740.01337285257530.4849192610970.0795926902160.224515309351-22.974493856718.8356075359-1.14713220972
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 13 through 23 )
2X-RAY DIFFRACTION2chain 'A' and (resid 24 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 55 )
4X-RAY DIFFRACTION4chain 'A' and (resid 56 through 75 )
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 101 )
6X-RAY DIFFRACTION6chain 'A' and (resid 102 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 149 )

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