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- PDB-3elc: Crystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 3elc
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with ligand
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / MECDP-synthase / Isoprene biosynthesis / Magnesium / Manganese / Metal-binding
Function / homology
Function and homology information


ubiquinone biosynthetic process / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / manganese ion binding / zinc ion binding / identical protein binding / 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
Chem-F01 / GERANYL DIPHOSPHATE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsHunter, W.N. / Ramsden, N.L. / Ulaganathan, V.
CitationJournal: J.Med.Chem. / Year: 2009
Title: A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy
Authors: Ramsden, N.L. / Buetow, L. / Dawson, A. / Kemp, L.A. / Ulaganathan, V. / Brenk, R. / Klebe, G. / Hunter, W.N.
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,02310
Polymers52,7293
Non-polymers1,2947
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-136 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.676, 54.833, 88.506
Angle α, β, γ (deg.)90.00, 99.66, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECPS / MECDP-synthase


Mass: 17576.275 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ispF / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P62617, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-F01 / 4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-fluoro-pyrimidin-2-one / 4-amino-5-fluoro-1-((2R,3S,4R,5R)-tetrahydro-3,4-dihydroxy-5-(hydroxymethyl)furan-2-yl)pyrimidin-2(1H)-one


Mass: 261.207 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H12FN3O5
#4: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.37 Å3/Da / Density % sol: 48.2 % / Description: The file contains Friedel pairs.
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10% glycerol, magnesium sulphate, 20% PEG 4000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 11, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 15989 / % possible obs: 47.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.2
Reflection shellResolution: 2.5→2.57 Å / % possible all: 91.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
CrystalCleardata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GX1

1gx1


Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.886 / Occupancy max: 1 / Occupancy min: 0 / SU B: 12.945 / SU ML: 0.286 / Cross valid method: THROUGHOUT / σ(F): 2.2 / ESU R: 1.648 / ESU R Free: 0.375 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: The file contains Friedel pairs.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 814 5.1 %RANDOM
Rwork0.208 ---
all0.289 15989 --
obs0.213 15127 91.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 86.53 Å2 / Biso mean: 48.536 Å2 / Biso min: 20 Å2
Baniso -1Baniso -2Baniso -3
1-7.45 Å20 Å2-0.88 Å2
2---3 Å20 Å2
3----4.75 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 76 113 3735
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223637
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9934939
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7765474
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25723.38142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.53615569
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3841524
X-RAY DIFFRACTIONr_chiral_restr0.0850.2566
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022734
X-RAY DIFFRACTIONr_nbd_refined0.2210.21718
X-RAY DIFFRACTIONr_nbtor_refined0.3030.22478
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0930.21
X-RAY DIFFRACTIONr_mcbond_it0.6871.52385
X-RAY DIFFRACTIONr_mcangle_it1.08623680
X-RAY DIFFRACTIONr_scbond_it1.34731404
X-RAY DIFFRACTIONr_scangle_it2.1824.51256
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.432 45 -
Rwork0.282 1033 -
all-1078 -
obs--83.37 %

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