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- PDB-4nan: Arabidopsis thaliana IspD in complex with tetrabromo-pseudilin -

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Basic information

Entry
Database: PDB / ID: 4nan
TitleArabidopsis thaliana IspD in complex with tetrabromo-pseudilin
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / herbicide / anti-infectives / pseudilin / natural product / drug discovery / allosteric inhibition / Rossmann Fold / Transferase / TRANSFERASE-TRANSFERASE INHIBITOR complex
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
2-bromo-6-(3,4,5-tribromo-1H-pyrrol-2-yl)phenol / : / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / 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
AuthorsKunfermann, A. / Witschel, M. / Illarionov, B. / Martin, R. / Rottmann, M. / Hoffken, H.W. / Seet, M. / Eisenreich, W. / Knolker, H.-J. / Fischer, M. ...Kunfermann, A. / Witschel, M. / Illarionov, B. / Martin, R. / Rottmann, M. / Hoffken, H.W. / Seet, M. / Eisenreich, W. / Knolker, H.-J. / Fischer, M. / Bacher, A. / Groll, M. / Diederich, F.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Pseudilins: Halogenated, Allosteric Inhibitors of the Non-Mevalonate Pathway Enzyme IspD.
Authors: Kunfermann, A. / Witschel, M. / Illarionov, B. / Martin, R. / Rottmann, M. / Hoffken, H.W. / Seet, M. / Eisenreich, W. / Knolker, H.J. / Fischer, M. / Bacher, A. / Groll, M. / Diederich, F.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2May 21, 2014Group: Database references
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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_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 4-phosphate cytidylyltransferase, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,77914
Polymers25,4301
Non-polymers1,34913
Water1,45981
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)53,55828
Polymers50,8602
Non-polymers2,69726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area3130 Å2
ΔGint-14 kcal/mol
Surface area19990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.120, 75.120, 224.130
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-408-

K

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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


Mass: 25430.193 Da / Num. of mol.: 1 / Fragment: UNP residues 76-302 / Mutation: R149S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At2g02500, ISPD, MCT, MECT, MEPCT, T8K22.20 / Plasmid: pNCO113 / Production host: Escherichia coli (E. coli) / Strain (production host): M15
References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

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Non-polymers , 6 types, 94 molecules

#2: Chemical ChemComp-2JM / 2-bromo-6-(3,4,5-tribromo-1H-pyrrol-2-yl)phenol


Mass: 474.769 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H5Br4NO
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL / Dithiothreitol


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.39 Å3/Da / Density % sol: 48.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES, 50 mM CdSO4, 800 mM KAc, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 6, 2013
RadiationMonochromator: LN2 cooled fixed-exit. Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 22879 / % possible obs: 99.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 26.3
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.612 / Mean I/σ(I) obs: 3.6 / % possible all: 98.8

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Processing

Software
NameClassification
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4NAI

4nai


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.622 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.132 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24721 1144 5 %RANDOM
Rwork0.20673 ---
all0.211 22879 --
obs0.20876 21735 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.539 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20.18 Å20 Å2
2--0.18 Å2-0 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1627 0 35 81 1743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191704
X-RAY DIFFRACTIONr_bond_other_d0.0010.021642
X-RAY DIFFRACTIONr_angle_refined_deg2.3212.0192316
X-RAY DIFFRACTIONr_angle_other_deg0.91233809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575208
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.80825.88268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.68515299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.816155
X-RAY DIFFRACTIONr_chiral_restr0.1080.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211857
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 81 -
Rwork0.328 1547 -
obs--97.9 %

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