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- PDB-8qcc: E.coli IspE in complex with a ligand (1) -

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Basic information

Entry
Database: PDB / ID: 8qcc
TitleE.coli IspE in complex with a ligand (1)
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 kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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)63,59111
Polymers61,9072
Non-polymers1,6859
Water3,351186
1
A: 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7845
Polymers30,9531
Non-polymers8304
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)31,8086
Polymers30,9531
Non-polymers8555
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)142.570, 52.793, 90.253
Angle α, β, γ (deg.)90.000, 126.690, 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

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Components

#1: Protein 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase


Mass: 30953.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ispE / Production host: Escherichia coli (E. coli) / References: UniProt: B7LXC3
#2: 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
#3: Chemical ChemComp-UKO / ~{N}-[3-[4-azanyl-2-oxidanylidene-1-[(2~{R})-thiolan-2-yl]pyrimidin-5-yl]prop-2-ynyl]cyclopropanesulfonamide


Mass: 354.448 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H18N4O3S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 186 / 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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 4k; 200 mM 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: 0.97 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 25, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→57.16 Å / Num. obs: 41807 / % possible obs: 98.41 % / Redundancy: 10.2 % / Biso Wilson estimate: 37.59 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 15.5
Reflection shellResolution: 1.9→1.972 Å / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 10.2 / Num. unique obs: 3718

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→57.16 Å / SU ML: 0.2915 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.997
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2353 2044 4.89 %
Rwork0.1935 39728 -
obs0.1956 41772 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.86 Å2
Refinement stepCycle: LAST / Resolution: 1.9→57.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4314 0 105 186 4605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00894520
X-RAY DIFFRACTIONf_angle_d1.15256170
X-RAY DIFFRACTIONf_chiral_restr0.0627693
X-RAY DIFFRACTIONf_plane_restr0.0094791
X-RAY DIFFRACTIONf_dihedral_angle_d18.9266645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.4331980.38742215X-RAY DIFFRACTION82.73
1.95-20.35091500.33122587X-RAY DIFFRACTION97.58
2-2.050.32771390.27962665X-RAY DIFFRACTION99.5
2.05-2.110.34811140.23832684X-RAY DIFFRACTION99.54
2.11-2.180.28481190.22182651X-RAY DIFFRACTION99.25
2.18-2.260.32131420.21282675X-RAY DIFFRACTION99.58
2.26-2.350.26721380.21532635X-RAY DIFFRACTION99.57
2.35-2.450.26811330.2132693X-RAY DIFFRACTION99.72
2.45-2.580.32181340.2082669X-RAY DIFFRACTION99.72
2.58-2.750.27161480.21082676X-RAY DIFFRACTION99.82
2.75-2.960.29151570.21022674X-RAY DIFFRACTION99.65
2.96-3.260.26531410.20662687X-RAY DIFFRACTION99.89
3.26-3.730.18751240.18152726X-RAY DIFFRACTION99.89
3.73-4.690.17891660.15362700X-RAY DIFFRACTION99.97
4.69-57.160.19991410.16962791X-RAY DIFFRACTION99.76
Refinement TLS params.Method: refined / Origin x: 28.8277155162 Å / Origin y: 0.817466567138 Å / Origin z: 17.2741834254 Å
111213212223313233
T0.39466908847 Å2-0.0164948732548 Å2-0.0307084773129 Å2-0.263633600936 Å2-0.00161027219456 Å2--0.281316607854 Å2
L1.02586217846 °20.124519690304 °2-0.162496595172 °2-0.184314300168 °2-0.0438598075348 °2--0.158288177067 °2
S-0.0222525638561 Å °0.0514438898514 Å °-0.00416686972613 Å °0.00534215421321 Å °0.017427071915 Å °-0.0191923869781 Å °-0.0221647923025 Å °-0.00530591667438 Å °0.00977816848516 Å °
Refinement TLS groupSelection details: all

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