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- PDB-2ycm: Inhibitors of herbicidal target IspD -

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Basic information

Entry
Database: PDB / ID: 2ycm
TitleInhibitors of herbicidal target IspD
Components2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
KeywordsTRANSFERASE / HERBICIDE / ALLOSTERIC BINDING POCKET / NON-MEVALONATE-PATHWAY
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / chloroplast stroma / chloroplast
Similarity search - Function
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / : / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-30A / : / COPPER (II) ION / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHoeffken, H.W.
Citation
#1: Journal: FEBS J. / Year: 2006
Title: The Crystal Structure of a Plant 2C-Methyl-D- Erythritol 4-Phosphate Cytidylyltransferase Exhibits a Distinct Quaternary Structure Compared to Bacterial Homologues and a Possible Role in ...Title: The Crystal Structure of a Plant 2C-Methyl-D- Erythritol 4-Phosphate Cytidylyltransferase Exhibits a Distinct Quaternary Structure Compared to Bacterial Homologues and a Possible Role in Feedback Regulation for Cytidine Monophosphate.
Authors: Gabrielsen, M. / Kaiser, J. / Rohdich, F. / Eisenreich, W. / Laupitz, R. / Bacher, A. / Bond, C.S. / Hunter, W.N.
History
DepositionMar 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _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 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0267
Polymers25,2991
Non-polymers7276
Water1,67593
1
A: 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
hetero molecules

A: 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,05314
Polymers50,5982
Non-polymers1,45512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z1
Buried area2210 Å2
ΔGint-70 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.060, 75.060, 220.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLYLTRANSFERASE, CHLOROPLASTIC / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE / MEP CYTIDYLYLTRANSFERASE / ATMECT / ATMEPCT / MCT


Mass: 25299.000 Da / Num. of mol.: 1 / Fragment: CYTIDYLTRANSFERASE DOMAIN, RESIDUES 76-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PNCO113 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4
References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

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Non-polymers , 5 types, 99 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#5: Chemical ChemComp-30A / 6-BENZYL-5-CHLORO-7-HYDROXYPYRAZOLO[1,5-A]PYRIMIDINE-3-CARBOXYLIC ACID


Mass: 303.701 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H10ClN3O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.41 Å3/Da / Density % sol: 48.48 % / Description: NONE
Crystal growDetails: NATIVE CRYSTALS (SEE REMARK 1, PDB 1W77) WERE SOAKED WITH A SATURATED SOLUTION OF LIGAND

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.939272
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939272 Å / Relative weight: 1
ReflectionResolution: 1.8→36.5 Å / Num. obs: 22629 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.84
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 2.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YC3

2yc3


Resolution: 1.8→73.61 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.944 / SU B: 6.984 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.205 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE ELECTRON DENSITY MAP SUGGESTS THAT IN THE CRYSTAL THE ALLOSTERIC POCKET IS ONLY PARTIALLY OCCUPIED AND ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. THE ELECTRON DENSITY MAP SUGGESTS THAT IN THE CRYSTAL THE ALLOSTERIC POCKET IS ONLY PARTIALLY OCCUPIED AND THEREFOR THE ELECTRON DENSITY REFLECTS AN OVERLAY OF THE UNLIGANDED AND LIGANDED ENZYME. THIS IS IN ACCORDANCE WITH THE HIGH TEMPERATURE FACTORS OF PART THE LIGAND AND OF THE AMINO ACIDS 264 TO 268 WHICH HAVE TO MOVE TO OPEN THE ALLOSTERIC BINDING POCKET.
RfactorNum. reflection% reflectionSelection details
Rfree0.23252 1132 5 %RANDOM
Rwork0.197 ---
obs0.19887 21497 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.227 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.24 Å20 Å2
2---0.49 Å20 Å2
3---0.73 Å2
Refinement stepCycle: LAST / Resolution: 1.8→73.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 26 93 1759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221708
X-RAY DIFFRACTIONr_bond_other_d0.0060.021114
X-RAY DIFFRACTIONr_angle_refined_deg1.9082.0032325
X-RAY DIFFRACTIONr_angle_other_deg1.03532761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9015214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.22726.23269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42515295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.879154
X-RAY DIFFRACTIONr_chiral_restr0.1120.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211875
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9031.51075
X-RAY DIFFRACTIONr_mcbond_other0.571.5428
X-RAY DIFFRACTIONr_mcangle_it3.12421751
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.6543633
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.0624.5574
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.02832822
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 82 -
Rwork0.225 1557 -
obs--99.94 %

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