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- PDB-5mrp: Arabidopsis thaliana IspD Glu258Ala mutant in complex with Azolop... -

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Basic information

Entry
Database: PDB / ID: 5mrp
TitleArabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (2)
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
KeywordsTRANSFERASE / herbicide / anti-infectives / drug discovery / allosteric inhibition / mutant
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-6BC / : / : / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSchwab, A. / Illarionov, B. / Frank, A. / Kunfermann, A. / Seet, M. / Bacher, A. / Witschel, M. / Fischer, M. / Groll, M. / Diederich, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationSFB749 Germany
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Mechanism of Allosteric Inhibition of the Enzyme IspD by Three Different Classes of Ligands.
Authors: Schwab, A. / Illarionov, B. / Frank, A. / Kunfermann, A. / Seet, M. / Bacher, A. / Witschel, M.C. / Fischer, M. / Groll, M. / Diederich, F.
History
DepositionDec 23, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_symmetry

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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)26,0727
Polymers25,3721
Non-polymers7006
Water1,51384
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)52,14514
Polymers50,7442
Non-polymers1,40012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area4090 Å2
ΔGint-35 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.990, 74.990, 221.720
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-406-

CD

21A-582-

HOH

31A-584-

HOH

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Components

#1: Protein 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, chloroplastic / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase / AtMEPCT


Mass: 25372.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated mutant (delta 1-74 / R149S) Glu258Ala Mutant
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: ISPD, MCT, MECT, MEPCT, At2g02500, T8K22.20 / Production host: Escherichia coli (E. coli)
References: UniProt: P69834, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical ChemComp-6BC / 5-chloro-7-hydroxy-6-(phenylmethyl)pyrazolo[1,5-a]pyrimidine-3-carbonitrile


Mass: 284.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H9ClN4O
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.36 Å3/Da / Density % sol: 47.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6 / Details: 50 mM HEPES, 50 mM CdSO4, 800 mM KAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19377 / % possible obs: 100 % / Redundancy: 11 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.6
Reflection shellResolution: 1.9→2 Å / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 5.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MRO

5mro


Resolution: 1.9→15 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.956 / SU B: 9.082 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23461 966 5 %RANDOM
Rwork0.20389 ---
obs0.20544 18358 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 47.614 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.25 Å2-0 Å2
2---0.49 Å2-0 Å2
3---1.59 Å2
Refinement stepCycle: 1 / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1629 0 25 84 1738
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021679
X-RAY DIFFRACTIONr_bond_other_d0.0030.021635
X-RAY DIFFRACTIONr_angle_refined_deg1.412.0052279
X-RAY DIFFRACTIONr_angle_other_deg0.9473.0023790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8335206
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15725.82167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.04815297
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.19155
X-RAY DIFFRACTIONr_chiral_restr0.0760.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211831
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02325
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_it2.4313.596833
X-RAY DIFFRACTIONr_mcbond_other2.4283.592832
X-RAY DIFFRACTIONr_mcangle_it2.7015.3621036
X-RAY DIFFRACTIONr_mcangle_other2.7045.3671037
X-RAY DIFFRACTIONr_scbond_it2.0864.057846
X-RAY DIFFRACTIONr_scbond_other2.0844.055847
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3395.8961244
X-RAY DIFFRACTIONr_long_range_B_refined3.10442.7241780
X-RAY DIFFRACTIONr_long_range_B_other3.09642.6771779
X-RAY DIFFRACTIONr_rigid_bond_restr1.37833312
X-RAY DIFFRACTIONr_sphericity_free21.161552
X-RAY DIFFRACTIONr_sphericity_bonded5.86653321
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 69 -
Rwork0.254 1323 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.6475 Å / Origin y: 25.4642 Å / Origin z: -19.6072 Å
111213212223313233
T0.0758 Å20.042 Å2-0.0104 Å2-0.0691 Å2-0.014 Å2--0.1379 Å2
L0.2679 °20.3614 °20.0605 °2-0.5055 °20.0131 °2--0.3352 °2
S-0.0019 Å °0.013 Å °-0.1857 Å °0.0274 Å °0.0358 Å °-0.2474 Å °-0.1467 Å °-0.109 Å °-0.0339 Å °

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