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- PDB-6e2w: MDDEF in complex with MVAPP, ADP, sulfate and cobalt -

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Basic information

Entry
Database: PDB / ID: 6e2w
TitleMDDEF in complex with MVAPP, ADP, sulfate and cobalt
ComponentsMevalonate diphosphate decarboxylase
KeywordsLYASE / Mevalonate diphosphate decarboxylase
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / transferase activity / ATP binding / metal ion 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
ADENOSINE-5'-DIPHOSPHATE / : / Chem-DP6 / diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsStauffacher, C.V. / Chen, C.-L.
CitationJournal: Nat Commun / Year: 2020
Title: Visualizing the enzyme mechanism of mevalonate diphosphate decarboxylase.
Authors: Chen, C.L. / Paul, L.N. / Mermoud, J.C. / Steussy, C.N. / Stauffacher, C.V.
History
DepositionJul 12, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 19, 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 1.2Oct 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: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2266
Polymers39,2761
Non-polymers9495
Water3,369187
1
A: Mevalonate diphosphate decarboxylase
hetero molecules

A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,45112
Polymers78,5532
Non-polymers1,89810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area5470 Å2
ΔGint-156 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.997, 98.071, 45.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-685-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mevalonate diphosphate decarboxylase / Diphosphomevalonate decarboxylase


Mass: 39276.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: mvaD, B6S42_02310 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FD68, diphosphomevalonate decarboxylase

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Non-polymers , 5 types, 192 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: 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 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.29 Å3/Da / Density % sol: 46.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Crystals were produced under the conditions of 1.6 M ammonium sulfate, 50 mM sodium acetate, pH 4.6; buffer exchange was performed under the conditions of 26 % PEG 3350, 5 mM CoCl2 and 50 mM ...Details: Crystals were produced under the conditions of 1.6 M ammonium sulfate, 50 mM sodium acetate, pH 4.6; buffer exchange was performed under the conditions of 26 % PEG 3350, 5 mM CoCl2 and 50 mM sodium acetate, pH 4.6; Crystals were soaked with MVAPP (200 micromole), followed by ATPgS (200 micromole). Then condensation was conducted at 30 % PEG 3350, 15% PEG 400, 5 mM CoCl2, 50 mM sodium acetate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 27047 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rpim(I) all: 0.022 / Net I/σ(I): 37.8
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 2630 / CC1/2: 0.917 / Rpim(I) all: 0.201 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5V2L

5v2l


Resolution: 1.95→33.513 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 21.5
RfactorNum. reflection% reflection
Rfree0.2192 1374 5.19 %
Rwork0.1955 --
obs0.1968 26481 97.85 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 1.95→33.513 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 52 187 2767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012631
X-RAY DIFFRACTIONf_angle_d1.0033569
X-RAY DIFFRACTIONf_dihedral_angle_d14.198938
X-RAY DIFFRACTIONf_chiral_restr0.053392
X-RAY DIFFRACTIONf_plane_restr0.006454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9498-2.01950.2891110.25472212X-RAY DIFFRACTION88
2.0195-2.10030.31581420.23932510X-RAY DIFFRACTION99
2.1003-2.19590.23671280.22382534X-RAY DIFFRACTION100
2.1959-2.31170.2681380.21192518X-RAY DIFFRACTION100
2.3117-2.45650.25531380.19972525X-RAY DIFFRACTION100
2.4565-2.6460.23741380.19792557X-RAY DIFFRACTION100
2.646-2.91220.24431160.19982560X-RAY DIFFRACTION100
2.9122-3.33330.2221370.20472577X-RAY DIFFRACTION100
3.3333-4.19830.19361730.17352546X-RAY DIFFRACTION99
4.1983-33.51790.1591530.16682568X-RAY DIFFRACTION95

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