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

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Basic information

Entry
Database: PDB / ID: 3fba
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


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 / metal ion binding / identical protein 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-C6B / GERANYL DIPHOSPHATE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å
AuthorsHunter, W.N. / Ramsden, N.L.
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
DepositionNov 19, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / 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_conn / struct_conn_type / 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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 25, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / struct_conn / struct_conn_type

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3715
Polymers17,5761
Non-polymers7954
Water66737
1
A: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules

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

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


Theoretical massNumber of molelcules
Total (without water)55,11415
Polymers52,7293
Non-polymers2,38512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_665-z+3/2,-x+1,y+1/21
crystal symmetry operation10_646-y+1,z-1/2,-x+3/21
Buried area9370 Å2
ΔGint-135.8 kcal/mol
Surface area16830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.127, 144.127, 144.127
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 17576.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ispF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / 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, 41 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-C6B / [(2S,3S,4R,5S)-5-(4-amino-2-oxo-pyrimidin-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 7.1 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.2M potassium sodium tartate tetrahydrate, tri-sodium citrate dihydrate, pH5.6, 2.0M ammonium sulphate, 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 Q210 2D / Detector: CCD / Date: Apr 1, 2004 / 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: 3.1→29.42 Å / Num. all: 9187 / Num. obs: 9178 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 0 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 6.188
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.1-3.2712.50.3262.31644213180.326100
3.27-3.4712.40.2123.51572912640.212100
3.47-3.7112.50.1474.71461111730.147100
3.71-412.30.1175.81360311020.117100
4-4.3812.40.0887.31243010060.088100
4.38-4.912.20.0758.4114989390.075100
4.9-5.6612.10.0718.799138190.071100
5.66-6.9311.90.0737.883006990.073100
6.93-9.811.20.0638.861285470.063100
9.8-29.429.90.0658.530793110.06596.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.1.20data scaling
AMoREphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GX1

1gx1


Resolution: 3.1→24.72 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.193 / WRfactor Rwork: 0.182 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.886 / SU B: 9.148 / SU ML: 0.164 / SU R Cruickshank DPI: 0.344 / SU Rfree: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.344 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.198 436 4.8 %RANDOM
Rwork0.186 ---
all0.187 9187 --
obs0.187 9160 99.91 %-
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: 90.56 Å2 / Biso mean: 55.168 Å2 / Biso min: 20 Å2
Refinement stepCycle: LAST / Resolution: 3.1→24.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 47 37 1267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221247
X-RAY DIFFRACTIONr_angle_refined_deg1.6122.0131690
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3915159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95323.12548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27715198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.927159
X-RAY DIFFRACTIONr_chiral_restr0.1180.2193
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02924
X-RAY DIFFRACTIONr_nbd_refined0.2120.2557
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2838
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.258
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.29
X-RAY DIFFRACTIONr_mcbond_it0.5471.5793
X-RAY DIFFRACTIONr_mcangle_it0.97421234
X-RAY DIFFRACTIONr_scbond_it1.1363497
X-RAY DIFFRACTIONr_scangle_it1.9024.5455
LS refinement shellResolution: 3.1→3.179 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 32 -
Rwork0.24 594 -
all-626 -
obs--100 %

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