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- PDB-6ypf: NUDIX1 hydrolase from Rosa x hybrida in complex with geranyl pyro... -

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Basic information

Entry
Database: PDB / ID: 6ypf
TitleNUDIX1 hydrolase from Rosa x hybrida in complex with geranyl pyrophosphate
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 / Geranyl diphosphate phosphohydrolase
Similarity search - Component
Biological speciesRosa hybrid cultivar (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 16, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,1172
Polymers16,8031
Non-polymers3141
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area650 Å2
ΔGint2 kcal/mol
Surface area6860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.287, 49.287, 104.286
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-375-

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 BL21(DE3) (bacteria) / Variant (production host): Rosetta
References: UniProt: M4I1C6, geranyl diphosphate phosphohydrolase
#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE / Geranyl pyrophosphate


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 200 mM ammonium sulfate, 100 mM sodium acetate , 25% PEG400, 5mM GPP (soaking 1s)

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.45→104.29 Å / Num. obs: 26639 / % possible obs: 99.46 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.75 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.05642 / Rpim(I) all: 0.029 / Net I/σ(I): 10.66
Reflection shellResolution: 1.45→1.502 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.05642 / Mean I/σ(I) obs: 0.69 / Num. unique obs: 2589 / CC1/2: 0.512 / CC star: 0.823 / Rpim(I) all: 0.02909 / % possible all: 98.69

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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: 1.45→42.68 Å / SU ML: 0.1984 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.8903
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 2007 7.55 %
Rwork0.207 24587 -
obs0.208 26594 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.67 Å2
Refinement stepCycle: LAST / Resolution: 1.45→42.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 19 109 1163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121102
X-RAY DIFFRACTIONf_angle_d1.01361501
X-RAY DIFFRACTIONf_chiral_restr0.0868158
X-RAY DIFFRACTIONf_plane_restr0.0072197
X-RAY DIFFRACTIONf_dihedral_angle_d16.7805157
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.490.40031370.37561672X-RAY DIFFRACTION98.37
1.49-1.530.38391430.33691723X-RAY DIFFRACTION99.2
1.53-1.570.33391400.30411720X-RAY DIFFRACTION99.52
1.57-1.620.28791400.28871744X-RAY DIFFRACTION99.63
1.62-1.680.27631400.2611723X-RAY DIFFRACTION99.36
1.68-1.750.28441450.27021751X-RAY DIFFRACTION99.74
1.75-1.830.25331460.2491730X-RAY DIFFRACTION99.58
1.83-1.920.2591460.22881747X-RAY DIFFRACTION99.68
1.92-2.040.22061400.22221764X-RAY DIFFRACTION99.69
2.04-2.20.20121450.2011736X-RAY DIFFRACTION99.73
2.2-2.420.21721440.19421780X-RAY DIFFRACTION99.69
2.42-2.770.21171450.19471787X-RAY DIFFRACTION99.74
2.77-3.490.19141490.18351810X-RAY DIFFRACTION99.49
3.5-42.680.19331470.18271900X-RAY DIFFRACTION99.03
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)
14.156733578064.41112240994.649271079974.858254660284.493780896117.283317615490.0744973910024-0.0300499857448-0.405290363162-0.2915469848320.07000001504030.06392962579990.743639289776-0.228700229688-0.1330328096730.357092610868-0.0196524583567-0.08253044156530.2052109226160.02580962902060.251852380033-34.06942504312.65981550013.8520613891
25.21336333682-0.2422109943830.389335091378.47062469995-0.2323207557214.107181446020.1571140338580.0679080316928-0.329796462055-0.975421400461-0.504213596008-0.5920181685940.5043730983790.6861288774070.2996876640390.3383275687210.135198159230.04733829151640.3738823639610.1205635779710.2267970953-20.640257370411.57695879428.48487438915
36.08169710021-1.397199190082.231717502211.82195822921-2.029975105374.39395190470.0906396979229-0.152866798647-0.08278267166670.01998588567630.04229590214270.04150394913780.30342135614-0.103964754153-0.148352158140.1844247968250.0175751534713-0.01522465319490.1200878053370.002010437881140.147262756895-34.647669771314.01554912414.1016371519
42.52410566518-0.7216696922012.343708812851.19019770526-1.346073232845.773141154620.1176363008050.0414851474039-0.0343824544809-0.0328409866214-0.07317293068660.04605749405540.2031536760810.274030706233-0.03635880674130.1729995626510.0212326417805-0.02408378839950.1416440974240.005810265941730.177303444284-29.462760110617.08144385198.10463817313
51.729425827972.97407759006-0.9098469174085.4263301637-2.111106927913.35137081158-0.002284468182560.270954069020.0887254690459-0.481529022455-0.0516892234223-0.1074323938710.6050346097020.1858770555380.08725988453860.2164007623470.1259580999360.002383283865050.2751741660610.06804158133780.281811356517-21.78903260736.3709414849813.7125113363
64.682075679541.28107126645-0.2616931332455.397090033720.3981553039543.5365671507-0.01524717677231.265297083040.637204203082-0.5829435262940.0412187612884-0.9526251068510.257037832061.59216902335-0.1018683340340.3233642882420.1696601310950.1028546913310.7625590288650.1481492401860.598867261905-15.840668686615.48525994062.9221430228
74.84623433633-0.472194548835-0.733398819646.065334803410.8340557552375.984088573340.1482284942690.112769759149-0.292189893577-0.211271456483-0.3695991472920.0362798688364-0.3429510053170.7122421945480.1949587383780.3443311205910.00913817665931-0.02692149696010.564410153090.08933446130630.331336477848-23.122692312919.1378769978-1.09583117958
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 46 )
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 111 )
5X-RAY DIFFRACTION5chain 'A' and (resid 112 through 124 )
6X-RAY DIFFRACTION6chain 'A' and (resid 125 through 134 )
7X-RAY DIFFRACTION7chain 'A' and (resid 135 through 149 )

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