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- PDB-6e2s: apo form of MDDEF with buffer exchange -

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Basic information

Entry
Database: PDB / ID: 6e2s
Titleapo form of MDDEF with buffer exchange
ComponentsMevalonate diphosphate decarboxylase
KeywordsLYASE / Mevalonate diphosphate decarboxylase
Function / homology
Function and homology information


diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase 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
diphosphomevalonate decarboxylase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.791 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)39,3722
Polymers39,2761
Non-polymers961
Water4,179232
1
A: Mevalonate diphosphate decarboxylase
hetero molecules

A: Mevalonate diphosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7454
Polymers78,5532
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area2090 Å2
ΔGint-50 kcal/mol
Surface area25530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.351, 97.872, 45.689
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#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
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.34 Å3/Da / Density % sol: 47.52 %
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 MgCl2 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 MgCl2 and 50 mM sodium acetate, pH 4.6, and then condensation was conducted at 30 % PEG 3350, 15% PEG 400, 5 mM MgCl2, 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: 1.791→50 Å / Num. obs: 35297 / % possible obs: 99.2 % / Redundancy: 7 % / Rpim(I) all: 0.025 / Net I/σ(I): 32.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3477 / CC1/2: 0.926 / Rpim(I) all: 0.206 / % 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: 1.791→33.396 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.85
RfactorNum. reflection% reflection
Rfree0.2255 1719 4.97 %
Rwork0.1879 --
obs0.1897 34580 97.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.791→33.396 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2416 0 5 232 2653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052672
X-RAY DIFFRACTIONf_angle_d0.7883615
X-RAY DIFFRACTIONf_dihedral_angle_d16.205967
X-RAY DIFFRACTIONf_chiral_restr0.048399
X-RAY DIFFRACTIONf_plane_restr0.006464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.791-1.84370.30791420.25592228X-RAY DIFFRACTION81
1.8437-1.90320.28661460.23042680X-RAY DIFFRACTION98
1.9032-1.97120.28481410.232765X-RAY DIFFRACTION99
1.9712-2.05020.25931430.21222770X-RAY DIFFRACTION100
2.0502-2.14340.25461360.20282776X-RAY DIFFRACTION100
2.1434-2.25640.24281610.19012775X-RAY DIFFRACTION100
2.2564-2.39780.25411440.19022772X-RAY DIFFRACTION100
2.3978-2.58280.20091330.18562815X-RAY DIFFRACTION100
2.5828-2.84260.2541460.18382823X-RAY DIFFRACTION100
2.8426-3.25370.22881280.19412819X-RAY DIFFRACTION99
3.2537-4.09810.20591540.16552845X-RAY DIFFRACTION99
4.0981-33.40170.16871450.17032793X-RAY DIFFRACTION93

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