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- PDB-2pmp: Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase... -

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Basic information

Entry
Database: PDB / ID: 2pmp
TitleStructure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from the isoprenoid biosynthetic pathway of Arabidopsis thaliana
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / Plant enzymes / Arabidopsis thaliana / MEP pathway / Isoprenoid-binding proteins / CMP / Zinc ions
Function / homology
Function and homology information


carotenoid biosynthetic process / chlorophyll biosynthetic process / 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 / chloroplast stroma / chloroplast / 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
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCalisto, B.M. / Perez-Gil, J. / Querol-Audi, J. / Fita, I. / Imperial, S.
CitationJournal: Protein Sci. / Year: 2007
Title: Biosynthesis of isoprenoids in plants: Structure of the 2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase from Arabidopsis thaliana. Comparison with the bacterial enzymes.
Authors: Calisto, B.M. / Perez-Gil, J. / Bergua, M. / Querol-Audi, J. / Fita, I. / Imperial, S.
History
DepositionApr 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8685
Polymers17,3491
Non-polymers5194
Water1,22568
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)53,60415
Polymers52,0473
Non-polymers1,55712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area9260 Å2
ΔGint-179 kcal/mol
Surface area17170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)135.795, 135.795, 135.795
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number214
Space group name H-MI4132
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: z, x, y and y, z, x.

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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: 17349.080 Da / Num. of mol.: 1 / Fragment: IspF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Strain: Ecotype Columbia 0 / Gene: ISPF / Plasmid: pET23b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) [pLysS]
References: UniProt: Q9CAK8, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 5 types, 72 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N3O8P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 3.01 Å3/Da / Density % sol: 59.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% PEG3350, 100mM MES, 200mM Ammonium Dihydrogen Phosphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0358 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 24, 2006 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0358 Å / Relative weight: 1
ReflectionResolution: 2.3→19.6 Å / Num. all: 9624 / Num. obs: 9624 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 19.6 % / Biso Wilson estimate: 56 Å2 / Rsym value: 0.057 / Net I/σ(I): 7
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 3.3 % / Num. unique all: 602 / Rsym value: 0.422 / % possible all: 89.67

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GX1
Resolution: 2.3→19.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.939 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.272 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 468 4.9 %RANDOM
Rwork0.198 ---
all0.2 9150 --
obs0.2 9150 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.3 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1220 0 28 68 1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221271
X-RAY DIFFRACTIONr_bond_other_d0.0040.02863
X-RAY DIFFRACTIONr_angle_refined_deg1.5072.0111726
X-RAY DIFFRACTIONr_angle_other_deg0.98432123
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1865159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.1723.95848
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60915219
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.949157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02230
X-RAY DIFFRACTIONr_nbd_refined0.1930.2237
X-RAY DIFFRACTIONr_nbd_other0.1990.2849
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2597
X-RAY DIFFRACTIONr_nbtor_other0.0870.2681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.254
X-RAY DIFFRACTIONr_metal_ion_refined0.0340.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1040.212
X-RAY DIFFRACTIONr_mcbond_it1.2321.51038
X-RAY DIFFRACTIONr_mcbond_other0.1361.5324
X-RAY DIFFRACTIONr_mcangle_it1.35621282
X-RAY DIFFRACTIONr_scbond_it1.8413531
X-RAY DIFFRACTIONr_scangle_it2.6624.5444
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 23 -
Rwork0.198 602 -
obs-625 89.67 %

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