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

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Basic information

Entry
Database: PDB / ID: 3ern
TitleCrystal structure of 2C-methyl-D-erythritol 2,4-clycodiphosphate synthase complexed with AraCMP
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / MECDP-synthase / Isoprene biosynthesis / Magnesium / Manganese / Metal-binding
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 / ubiquinone biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 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
CYTOSINE ARABINOSE-5'-PHOSPHATE / GERANYL DIPHOSPHATE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHunter, W.N. / Ramsden, N.L. / Kemp, L.A.
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
DepositionOct 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...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 / 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

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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
D: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,15619
Polymers105,4586
Non-polymers2,69813
Water5,116284
1
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)54,24010
Polymers52,7293
Non-polymers1,5117
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8670 Å2
ΔGint-135 kcal/mol
Surface area17410 Å2
MethodPISA
2
D: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9169
Polymers52,7293
Non-polymers1,1876
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-132 kcal/mol
Surface area17070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.856, 54.236, 118.384
Angle α, β, γ (deg.)90.000, 94.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 17576.275 Da / Num. of mol.: 6
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

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Non-polymers , 5 types, 297 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CAR / CYTOSINE ARABINOSE-5'-PHOSPHATE


Type: RNA linking / Mass: 323.197 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE / Geranyl pyrophosphate


Mass: 314.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O7P2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.69 Å3/Da / Density % sol: 54.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1M ammonium sulfate, sodium acetate, PEG 2000 MME, pH 4.4, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 1, 2003 / Details: mirrors
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 71490 / Num. obs: 65677 / % possible obs: 91.86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1.6 / Redundancy: 4.6 % / Rsym value: 0.089
Reflection shellResolution: 2.1→2.154 Å / % possible all: 92.95

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GX1

1gx1


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.223 / WRfactor Rwork: 0.207 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.806 / SU B: 5.691 / SU ML: 0.148 / SU R Cruickshank DPI: 0.222 / SU Rfree: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3342 5.1 %RANDOM
Rwork0.218 ---
obs0.219 65677 99.34 %-
all-66113 --
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: 96.14 Å2 / Biso mean: 34.02 Å2 / Biso min: 15.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å2-0.57 Å2
2---3.18 Å20 Å2
3---4.66 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6975 0 157 284 7416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227242
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9949813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465920
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.52123.515293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49151165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7131549
X-RAY DIFFRACTIONr_chiral_restr0.1280.21118
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.025400
X-RAY DIFFRACTIONr_nbd_refined0.1990.23289
X-RAY DIFFRACTIONr_nbtor_refined0.3020.24927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2393
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2150.210
X-RAY DIFFRACTIONr_mcbond_it0.7681.54678
X-RAY DIFFRACTIONr_mcangle_it1.24527256
X-RAY DIFFRACTIONr_scbond_it1.51432832
X-RAY DIFFRACTIONr_scangle_it2.5434.52557
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 224 -
Rwork0.297 4259 -
all-4483 -
obs--92.95 %

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