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- PDB-1iv1: Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase -

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Basic information

Entry
Database: PDB / ID: 1iv1
TitleStructure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / isoprenoid / non-mevalonate / synthase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding
Similarity search - Function
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsKishida, H. / Wada, T. / Unzai, S. / Kuzuyama, T. / Terada, T. / Sirouzu, M. / Yokoyama, S. / Tame, J.R.H. / Park, S.-Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.
Authors: Kishida, H. / Wada, T. / Unzai, S. / Kuzuyama, T. / Takagi, M. / Terada, T. / Shirouzu, M. / Yokoyama, S. / Tame, J.R. / Park, S.Y.
History
DepositionMar 11, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
D: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
E: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
F: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase


Theoretical massNumber of molelcules
Total (without water)99,2646
Polymers99,2646
Non-polymers00
Water6,341352
1
A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
D: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase


Theoretical massNumber of molelcules
Total (without water)49,6323
Polymers49,6323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-7 kcal/mol
Surface area17100 Å2
MethodPISA
2
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
E: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
F: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase


Theoretical massNumber of molelcules
Total (without water)49,6323
Polymers49,6323
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-8 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.828, 105.828, 148.674
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
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase /


Mass: 16544.078 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: PET11B / Production host: Escherichia coli (E. coli)
References: UniProt: Q8RQP5, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.1 Å3/Da / Density % sol: 41.31 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5 / Details: PEG, pH 6.5, EVAPORATION, temperature 298K
Crystal grow
*PLUS
Temperature: 293 K / pH: 8 / Method: vapor diffusion, hanging drop / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15.1 mg/mlprotein1drop
220 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
41 mMdithiothreitol1drop
550 mMTris-HCl1reservoirpH8.5
61.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 0.7 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 20, 2001 / Details: mirrors
RadiationMonochromator: SI-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.65→15 Å / Num. all: 935741 / Num. obs: 97488 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 9.6 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 7.2
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.26 / % possible all: 73.8
Reflection
*PLUS
Lowest resolution: 15 Å / Num. measured all: 935741
Reflection shell
*PLUS
% possible obs: 73.8 % / Rmerge(I) obs: 0.26

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.65→20 Å / Num. parameters: 29175 / Num. restraintsaints: 28465 / Isotropic thermal model: Isotropic / Cross valid method: free R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.314 4880 -RANDOM
Rwork0.228 ---
all0.226 92608 --
obs-92608 91.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER,J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 7293
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 0 352 7264
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.023
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.033
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0247
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.083
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Num. reflection obs: 97488 / % reflection Rfree: 5.3 % / Rfactor Rfree: 0.312 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: s_angle_d / Dev ideal: 0.02

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