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- PDB-8xkf: Crystal structure of Helicobacter pylori IspDF with substrate CTP -

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Basic information

Entry
Database: PDB / ID: 8xkf
TitleCrystal structure of Helicobacter pylori IspDF with substrate CTP
ComponentsBifunctional enzyme IspD/IspF
KeywordsTRANSFERASE / IspD / IspF / Helicobacter pylori / CTP
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / metal ion binding
Similarity search - Function
Bifunctional enzyme IspD/IspF / 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. / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family ...Bifunctional enzyme IspD/IspF / 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. / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
CYTIDINE-5'-MONOPHOSPHATE / CYTIDINE-5'-DIPHOSPHATE / CYTIDINE-5'-TRIPHOSPHATE / Bifunctional enzyme IspD/IspF
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, X. / Wu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int J Antimicrob Agents / Year: 2024
Title: Two natural compounds as potential inhibitors against the Helicobacter pylori and Acinetobacter baumannii IspD enzymes.
Authors: Chen, X. / Zhao, H. / Wang, C. / Hamed, M. / Shang, Q. / Yang, Y. / Diao, X. / Sun, X. / Hu, W. / Jiang, X. / Zhang, Y. / Hirsch, A.K.H. / Wu, D. / Zhuang, J.
History
DepositionDec 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bifunctional enzyme IspD/IspF
B: Bifunctional enzyme IspD/IspF
C: Bifunctional enzyme IspD/IspF
D: Bifunctional enzyme IspD/IspF
E: Bifunctional enzyme IspD/IspF
F: Bifunctional enzyme IspD/IspF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,20833
Polymers257,3426
Non-polymers5,86627
Water12,124673
1
A: Bifunctional enzyme IspD/IspF
B: Bifunctional enzyme IspD/IspF
C: Bifunctional enzyme IspD/IspF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,56818
Polymers128,6713
Non-polymers2,89715
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12390 Å2
ΔGint-107 kcal/mol
Surface area47990 Å2
MethodPISA
2
D: Bifunctional enzyme IspD/IspF
E: Bifunctional enzyme IspD/IspF
F: Bifunctional enzyme IspD/IspF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,64015
Polymers128,6713
Non-polymers2,96912
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-128 kcal/mol
Surface area48010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.624, 146.624, 256.495
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Bifunctional enzyme IspD/IspF


Mass: 42890.289 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Gene: ispDF, HP_1020 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O25664, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 9 types, 700 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE


Mass: 483.156 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: C9H14N3O8P / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C9H15N3O11P2 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 673 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.15 Å3/Da / Density % sol: 60.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.5 M ammonium sulfate, 1.0 M lithium sufate, 0.1 M sodium citrate tribasic dihydrate (pH 5.6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 110587 / % possible obs: 99.8 % / Redundancy: 18 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.042 / Rrim(I) all: 0.181 / Χ2: 1.021 / Net I/σ(I): 4.4 / Num. measured all: 1990895
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.5-2.5416.31.31554350.7810.9360.3211.3551.01199.1
2.54-2.5916.91.20654230.8250.9510.2891.2410.99899.3
2.59-2.6417.21.07854510.8510.9590.2561.1091.00799.5
2.64-2.6917.20.91354500.8970.9720.2170.9391.04699.6
2.69-2.7516.60.82354760.9020.9740.20.8481.01999.7
2.75-2.8217.70.74754800.9280.9810.1760.7681.0399.8
2.82-2.8917.30.63654930.940.9850.1520.6551.02799.9
2.89-2.9617.50.53654670.9570.9890.1280.5511.038100
2.96-3.0518.20.45354970.970.9920.1060.4651.04699.9
3.05-3.1518.10.37254600.9810.9950.0880.3821.05100
3.15-3.2617.80.2955630.9860.9960.0690.2981.061100
3.26-3.3917.60.22155080.9920.9980.0530.2271.076100
3.39-3.5518.30.18955150.9950.9990.0450.1941.101100
3.55-3.7318.20.1555180.9960.9990.0360.1541.115100
3.73-3.9719.20.12155730.9970.9990.0280.1241.086100
3.97-4.27190.09655290.9980.9990.0230.0991.039100
4.27-4.719.30.08255950.99810.0190.0851.018100
4.7-5.3819.70.07856090.99910.0180.080.951100
5.38-6.7819.50.0856430.99810.0190.0820.893100
6.78-5018.30.05559020.99910.0130.0570.847100

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→47.56 Å / Cross valid method: THROUGHOUT / σ(F): 650.28 / Phase error: 23.33 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2273 5675 5.16 %
Rwork0.1924 --
obs0.1949 109920 99.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→47.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17578 0 354 673 18605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00818307
X-RAY DIFFRACTIONf_angle_d1.4324759
X-RAY DIFFRACTIONf_dihedral_angle_d13.3582402
X-RAY DIFFRACTIONf_chiral_restr0.0632783
X-RAY DIFFRACTIONf_plane_restr0.0153072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.34152460.25824953X-RAY DIFFRACTION90
2.54-2.590.28922820.24775045X-RAY DIFFRACTION92
2.59-2.640.30673040.24465102X-RAY DIFFRACTION93
2.64-2.690.28872780.23735144X-RAY DIFFRACTION94
2.69-2.750.25982610.23385183X-RAY DIFFRACTION95
2.75-2.820.27742900.23575175X-RAY DIFFRACTION94
2.82-2.890.28712570.22535218X-RAY DIFFRACTION95
2.89-2.960.24972430.21915222X-RAY DIFFRACTION96
2.96-3.050.28472800.21645217X-RAY DIFFRACTION95
3.05-3.150.25922480.21865211X-RAY DIFFRACTION95
3.15-3.260.26173700.20655187X-RAY DIFFRACTION93
3.26-3.390.23362710.19485238X-RAY DIFFRACTION95
3.39-3.550.23062860.18825220X-RAY DIFFRACTION95
3.55-3.730.2142580.17455264X-RAY DIFFRACTION95
3.73-3.970.19983210.16275241X-RAY DIFFRACTION94
3.97-4.270.18892820.15515251X-RAY DIFFRACTION95
4.27-4.70.16843130.15415273X-RAY DIFFRACTION94
4.7-5.380.20512800.17375325X-RAY DIFFRACTION95
5.38-6.780.23472980.21995340X-RAY DIFFRACTION95
6.78-47.560.19362860.17865457X-RAY DIFFRACTION93

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