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- PDB-4nak: Arabidopsis thaliana IspD in complex with pentabromo-pseudilin -

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Basic information

Entry
Database: PDB / ID: 4nak
TitleArabidopsis thaliana IspD in complex with pentabromo-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
: / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / : / PENTABROMOPSEUDILIN / 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_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_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.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

Downloads & links

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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)26,93514
Polymers25,4301
Non-polymers1,50513
Water1,24369
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)53,87028
Polymers50,8602
Non-polymers3,00926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area3090 Å2
ΔGint-8 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.240, 75.240, 224.140
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-404-

CD

21A-409-

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 / 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 , 5 types, 82 molecules

#2: Chemical ChemComp-PBQ / PENTABROMOPSEUDILIN


Mass: 553.665 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H4Br5NO / Comment: antibiotic*YM
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-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.: 5 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
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: Feb 9, 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: 22147 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 19.5
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.536 / Mean I/σ(I) obs: 3.3 / % possible all: 97.3

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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→10 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.67 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R: 0.201 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21821 1108 5 %RANDOM
Rwork0.19059 ---
all0.194 22147 --
obs0.19194 21039 95.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.488 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.42 Å20 Å2
2--0.42 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1631 0 36 69 1736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191684
X-RAY DIFFRACTIONr_angle_refined_deg1.052.0092286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8495206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40425.88268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.11915298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.245155
X-RAY DIFFRACTIONr_chiral_restr0.0640.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211226
X-RAY DIFFRACTIONr_rigid_bond_restr2.44331684
X-RAY DIFFRACTIONr_sphericity_free22.6531
X-RAY DIFFRACTIONr_sphericity_bonded9.37151706
LS refinement shellResolution: 1.8→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 79 -
Rwork0.195 1494 -
obs--96.86 %
Refinement TLS params.Method: refined / Origin x: 12.6668 Å / Origin y: 25.6812 Å / Origin z: -19.4394 Å
111213212223313233
T0.0117 Å20.0139 Å2-0.0125 Å2-0.0265 Å20.0083 Å2--0.0737 Å2
L0.2472 °20.2639 °20.021 °2-0.2892 °2-0.017 °2--0.3064 °2
S0.014 Å °-0.0223 Å °-0.1315 Å °0.0194 Å °-0.0311 Å °-0.145 Å °-0.0229 Å °-0.0415 Å °0.0171 Å °

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