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- PDB-6n10: Crystal structure of Arabidopsis thaliana mevalonate 5-diphosphat... -

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Basic information

Entry
Database: PDB / ID: 6n10
TitleCrystal structure of Arabidopsis thaliana mevalonate 5-diphosphate decarboxylase 1 complexed with (R)-MVAPP
ComponentsDiphosphomevalonate decarboxylase MVD1, peroxisomal
KeywordsLYASE
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / peroxisome / ATP binding / identical protein binding / cytosol
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / : / Diphosphomevalonate decarboxylase-like N-terminal domain / GHMP kinase, C-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-DP6 / Diphosphomevalonate decarboxylase MVD1, peroxisomal
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNoel, J.P. / Thomas, S.T. / Louie, G.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)EEC-0813570 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Substrate Specificity and Engineering of Mevalonate 5-Phosphate Decarboxylase.
Authors: Thomas, S.T. / Louie, G.V. / Lubin, J.W. / Lundblad, V. / Noel, J.P.
History
DepositionNov 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: 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: Diphosphomevalonate decarboxylase MVD1, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6186
Polymers45,9251
Non-polymers6925
Water1,820101
1
A: Diphosphomevalonate decarboxylase MVD1, peroxisomal
hetero molecules

A: Diphosphomevalonate decarboxylase MVD1, peroxisomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,23512
Polymers91,8502
Non-polymers1,38510
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4640 Å2
ΔGint-139 kcal/mol
Surface area33520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.630, 106.630, 166.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Diphosphomevalonate decarboxylase MVD1, peroxisomal / Mevalonate 5-diphosphate decarboxylase 1 / AtMVD1


Mass: 45925.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: MVD1, MDD1, MVD, At2g38700 / Production host: Escherichia coli (E. coli)
References: UniProt: O23722, diphosphomevalonate decarboxylase
#2: Chemical ChemComp-DP6 / (3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID


Mass: 308.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O10P2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic pH 5.6 0.2 M potassium sodium tartrate 2.0 M ammonium sulfate 5mM (R)-MVAPP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 4, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→53.315 Å / Num. obs: 42293 / % possible obs: 97.8 % / Redundancy: 10.7 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 13.1
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.536 / Num. unique obs: 2744 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260)refinement
MOSFLM7.1.0data reduction
Aimless0.2.7data scaling
MOLREP11.2.08phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D4J

3d4j


Resolution: 2.3→49.168 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.69
RfactorNum. reflection% reflection
Rfree0.2254 4793 6.03 %
Rwork0.1897 --
obs0.1918 42182 97.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.3→49.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 38 101 3276
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143230
X-RAY DIFFRACTIONf_angle_d1.4574377
X-RAY DIFFRACTIONf_dihedral_angle_d20.8121208
X-RAY DIFFRACTIONf_chiral_restr0.066492
X-RAY DIFFRACTIONf_plane_restr0.01559
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.32610.38431810.32532462X-RAY DIFFRACTION96
2.3261-2.35350.34871510.32622408X-RAY DIFFRACTION95
2.3535-2.38220.31911490.31562441X-RAY DIFFRACTION96
2.3822-2.41240.34931420.30382456X-RAY DIFFRACTION96
2.4124-2.44410.27821360.29022413X-RAY DIFFRACTION95
2.4441-2.47760.27731470.30342460X-RAY DIFFRACTION95
2.4776-2.5130.37591670.29452405X-RAY DIFFRACTION95
2.513-2.55050.33021610.27852421X-RAY DIFFRACTION95
2.5505-2.59030.3421570.26642423X-RAY DIFFRACTION95
2.5903-2.63280.31371600.25622389X-RAY DIFFRACTION94
2.6328-2.67820.28461520.24972365X-RAY DIFFRACTION94
2.6782-2.72690.28121590.23932407X-RAY DIFFRACTION94
2.7269-2.77930.26761580.24432428X-RAY DIFFRACTION96
2.7793-2.83610.24871470.23212517X-RAY DIFFRACTION98
2.8361-2.89770.29611720.22532478X-RAY DIFFRACTION98
2.8977-2.96510.29511640.23122573X-RAY DIFFRACTION100
2.9651-3.03930.25461630.2372509X-RAY DIFFRACTION100
3.0393-3.12140.26481740.21852537X-RAY DIFFRACTION100
3.1214-3.21330.24241580.22492569X-RAY DIFFRACTION100
3.2133-3.31690.25111620.20852520X-RAY DIFFRACTION100
3.3169-3.43550.21981670.19062567X-RAY DIFFRACTION100
3.4355-3.5730.24071690.18242536X-RAY DIFFRACTION100
3.573-3.73550.20561530.18952535X-RAY DIFFRACTION100
3.7355-3.93240.20981790.16252549X-RAY DIFFRACTION100
3.9324-4.17870.18481590.14342541X-RAY DIFFRACTION100
4.1787-4.50110.16011590.13412556X-RAY DIFFRACTION100
4.5011-4.95370.15191580.12772540X-RAY DIFFRACTION100
4.9537-5.66960.16921670.14452554X-RAY DIFFRACTION100
5.6696-7.13960.20891630.16212547X-RAY DIFFRACTION100
7.1396-49.1790.19111590.16042563X-RAY DIFFRACTION100

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