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- PDB-8qc7: New monoclinic EcIspE -

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Basic information

Entry
Database: PDB / ID: 8qc7
TitleNew monoclinic EcIspE
Components4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
KeywordsTRANSFERASE / E. coli / IspE / inhibitor / complex.
Function / homology
Function and homology information


4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase / 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / ATP binding
Similarity search - Function
4-diphosphocytidyl-2C-methyl-D-erythritol kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsHamid, R.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: Structure / Year: 2024
Title: IspE kinase as an anti-infective target: Role of a hydrophobic pocket in inhibitor binding.
Authors: Hamid, R. / Walsh, D.J. / Diamanti, E. / Aguilar, D. / Lacour, A. / Hamed, M.M. / Hirsch, A.K.H.
History
DepositionAug 25, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
B: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,0798
Polymers62,1332
Non-polymers1,9466
Water3,081171
1
A: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0394
Polymers31,0661
Non-polymers9733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0394
Polymers31,0661
Non-polymers9733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.196, 53.046, 91.070
Angle α, β, γ (deg.)90.000, 126.930, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-403-

HOH

21B-452-

HOH

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Components

#1: Protein 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase / CMK / 4-(cytidine-5'-diphospho)-2-C-methyl-D-erythritol kinase


Mass: 31066.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ispE, ECIAI1_1229 / Production host: Escherichia coli (E. coli)
References: UniProt: B7LXC3, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
#2: Chemical ChemComp-CDM / 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL


Mass: 521.308 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H25N3O14P2
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / Details: 25% PEG 4k; 200mM MgCl2; 100mM MES pH 6.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.93 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.03→35.39 Å / Num. obs: 35241 / % possible obs: 98.97 % / Redundancy: 3.9 % / Biso Wilson estimate: 26.82 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6
Reflection shellResolution: 2.03→2.103 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 3472 / % possible all: 98.52

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→35.39 Å / SU ML: 0.2727 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0384
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.24 1852 5.26 %
Rwork0.2164 33374 -
obs0.2177 35226 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.24 Å2
Refinement stepCycle: LAST / Resolution: 2.03→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4322 0 122 171 4615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00294560
X-RAY DIFFRACTIONf_angle_d0.756237
X-RAY DIFFRACTIONf_chiral_restr0.0447709
X-RAY DIFFRACTIONf_plane_restr0.0056794
X-RAY DIFFRACTIONf_dihedral_angle_d13.7162636
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.080.39211290.31572522X-RAY DIFFRACTION98.55
2.08-2.150.3341540.29532522X-RAY DIFFRACTION98.2
2.15-2.220.30451480.27982533X-RAY DIFFRACTION98.31
2.22-2.290.31281400.27422543X-RAY DIFFRACTION99.04
2.29-2.390.27391380.25762588X-RAY DIFFRACTION99.31
2.39-2.50.31661160.25492541X-RAY DIFFRACTION99.03
2.5-2.630.26951370.25022577X-RAY DIFFRACTION99.09
2.63-2.790.28311780.2442521X-RAY DIFFRACTION98.61
2.79-3.010.25211340.25092574X-RAY DIFFRACTION99.6
3.01-3.310.25811320.21922620X-RAY DIFFRACTION99.67
3.31-3.790.20281330.19112620X-RAY DIFFRACTION99.67
3.79-4.770.17641600.15822564X-RAY DIFFRACTION98.98
4.77-35.390.19331530.1692649X-RAY DIFFRACTION98.91
Refinement TLS params.Method: refined / Origin x: 28.6800740035 Å / Origin y: 0.727851476775 Å / Origin z: 17.4982954317 Å
111213212223313233
T0.342798301324 Å2-0.0130157779455 Å2-0.0175809266478 Å2-0.177803110292 Å20.00127162954759 Å2--0.174332599349 Å2
L0.997943031439 °20.0782455218374 °2-0.212804930282 °2-0.115224298803 °2-0.0206887434361 °2--0.246291958371 °2
S-0.00527352870706 Å °0.0423301384125 Å °0.0401329947936 Å °0.0316865851441 Å °0.0088958044041 Å °-0.0204295525552 Å °-0.0223755893453 Å °-0.00668800659147 Å °-0.00280693341181 Å °
Refinement TLS groupSelection details: all

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