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- PDB-1fi4: THE X-RAY CRYSTAL STRUCTURE OF MEVALONATE 5-DIPHOSPHATE DECARBOXY... -

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Basic information

Entry
Database: PDB / ID: 1fi4
TitleTHE X-RAY CRYSTAL STRUCTURE OF MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE AT 2.3 ANGSTROM RESOLUTION.
ComponentsMEVALONATE 5-DIPHOSPHATE DECARBOXYLASE
KeywordsLYASE / mixed alpha/beta structure / ATP binding / decarboxylase / cholesterol biosynthesis / structural genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Synthesis of Dolichyl-phosphate / Cholesterol biosynthesis / diphosphomevalonate decarboxylase / diphosphomevalonate decarboxylase activity / isopentenyl diphosphate biosynthetic process, mevalonate pathway / sterol biosynthetic process / ATP binding / cytosol / cytoplasm
Similarity search - Function
Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 ...Diphosphomevalonate decarboxylase / Mvd1, C-terminal / Mevalonate 5-diphosphate decarboxylase C-terminal domain / Diphosphomevalonate/phosphomevalonate decarboxylase / GHMP kinase, C-terminal domain / GHMP kinase N-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 speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.27 Å
AuthorsBonanno, J.B. / Edo, C. / Eswar, N. / Pieper, U. / Romanowski, M.J. / Ilyin, V. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Sali, A. ...Bonanno, J.B. / Edo, C. / Eswar, N. / Pieper, U. / Romanowski, M.J. / Ilyin, V. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Sali, A. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2001
Title: Structural genomics of enzymes involved in sterol/isoprenoid biosynthesis.
Authors: Bonanno, J.B. / Edo, C. / Eswar, N. / Pieper, U. / Romanowski, M.J. / Ilyin, V. / Gerchman, S.E. / Kycia, H. / Studier, F.W. / Sali, A. / Burley, S.K.
History
DepositionAug 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)46,8041
Polymers46,8041
Non-polymers00
Water2,954164
1
A: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE

A: MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE


Theoretical massNumber of molelcules
Total (without water)93,6082
Polymers93,6082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area2750 Å2
ΔGint-18 kcal/mol
Surface area31860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.796, 126.402, 47.242
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsphysiological dimer observed in crystal

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Components

#1: Protein MEVALONATE 5-DIPHOSPHATE DECARBOXYLASE / MDD / DIPHOSPHOMEVALONATE DECARBOXYLASE


Mass: 46804.043 Da / Num. of mol.: 1
Mutation: M1(MSE), M89(MSE), M169(MSE), M179(MSE), M192(MSE), M212(MSE), M237(MSE), M254(MSE), M255(MSE), M274(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Description: HIS-TAG MODIFIED PET28A PLASMID / Production host: Escherichia coli (E. coli)
References: UniProt: P32377, diphosphomevalonate decarboxylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris-HCl pH 8.5, 15% PEG 4K, 1M NaCl, 5% glycerol, 5% ethylene glycol, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1reservoir
215 %(w/v)PEG40001reservoir
31 M1reservoirNaCl
45 %(v/v)ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Oct 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. all: 41954 / Num. obs: 40942 / % possible obs: 97.6 % / Observed criterion σ(F): 9999 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 25
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.227 / Num. unique all: 4206 / % possible all: 90.8
Reflection
*PLUS
Lowest resolution: 18 Å / % possible obs: 99.1 % / Rmerge(I) obs: 0.03
Reflection shell
*PLUS
% possible obs: 90.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
CNS0.9refinement
RefinementResolution: 2.27→30 Å / σ(F): 9999 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: The model was refined against a target of maximum likelihood on solvent flattened phases except for the last round of Powell minimization when a target of maximum likelihood on F was used. ...Details: The model was refined against a target of maximum likelihood on solvent flattened phases except for the last round of Powell minimization when a target of maximum likelihood on F was used. The data were corrected for anomalous scattering by the selenium atoms.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 4094 -Random
Rwork0.239 ---
all0.242 41454 --
obs0.242 41454 100 %-
Refinement stepCycle: LAST / Resolution: 2.27→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3062 0 0 164 3226
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.683
X-RAY DIFFRACTIONc_bond_d0.0077
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 18 Å / σ(F): 9999 / Rfactor obs: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3

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