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

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Basic information

Entry
Database: PDB / ID: 5mro
TitleArabidopsis thaliana IspD Glu258Ala mutant in complex with Azolopyrimidine (1)
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
ACETATE ION / : / : / Azolopyrimidine / 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
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_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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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)26,1908
Polymers25,3721
Non-polymers8187
Water2,414134
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)52,38116
Polymers50,7442
Non-polymers1,63614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_554x-y+1/3,-y+2/3,-z-1/31
Buried area4770 Å2
ΔGint-38 kcal/mol
Surface area20610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.800, 74.800, 221.990
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-521-

HOH

21A-633-

HOH

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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 / 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

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Non-polymers , 6 types, 141 molecules

#2: Chemical ChemComp-Q9P / Azolopyrimidine


Mass: 260.679 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9ClN4O
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 18.015 Da / Num. of mol.: 134 / 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: 47.78 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / 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: 1.8→50 Å / Num. obs: 22644 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.2
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 5.2 / % 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: 2YC5

2yc5


Resolution: 1.8→15 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / SU B: 6.445 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.121 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22472 1130 5 %RANDOM
Rwork0.19771 ---
obs0.20099 21461 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.689 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å2-0.15 Å2-0 Å2
2---0.31 Å2-0 Å2
3---1 Å2
Refinement stepCycle: 1 / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 34 134 1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.021739
X-RAY DIFFRACTIONr_bond_other_d0.0030.021704
X-RAY DIFFRACTIONr_angle_refined_deg1.2962.0142360
X-RAY DIFFRACTIONr_angle_other_deg0.8983.0023946
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8325213
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05225.65269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15615311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.733156
X-RAY DIFFRACTIONr_chiral_restr0.0690.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211892
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02336
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_it1.6053.03859
X-RAY DIFFRACTIONr_mcbond_other1.5753.029857
X-RAY DIFFRACTIONr_mcangle_it1.8354.5281069
X-RAY DIFFRACTIONr_mcangle_other1.8564.5321070
X-RAY DIFFRACTIONr_scbond_it1.7763.495879
X-RAY DIFFRACTIONr_scbond_other1.7753.493880
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6665.0631291
X-RAY DIFFRACTIONr_long_range_B_refined2.73237.2671919
X-RAY DIFFRACTIONr_long_range_B_other2.58937.0111900
X-RAY DIFFRACTIONr_rigid_bond_restr0.67833437
X-RAY DIFFRACTIONr_sphericity_free22.223574
X-RAY DIFFRACTIONr_sphericity_bonded5.42453478
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 81 -
Rwork0.235 1529 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 12.1034 Å / Origin y: 25.2356 Å / Origin z: -20.2456 Å
111213212223313233
T0.063 Å20.048 Å2-0.0064 Å2-0.0563 Å2-0.0088 Å2--0.1027 Å2
L0.3103 °20.3482 °20.0692 °2-0.4212 °20.004 °2--0.2026 °2
S-0.0022 Å °0.0001 Å °-0.1773 Å °0.0427 Å °0.0301 Å °-0.2034 Å °-0.1078 Å °-0.0901 Å °-0.0278 Å °

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