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- PDB-8xkg: Crystal structure of Acinetobacter baumannii IspD -

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Basic information

Entry
Database: PDB / ID: 8xkg
TitleCrystal structure of Acinetobacter baumannii IspD
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / IspD / Acinetobacter baumannii / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
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 / terpenoid biosynthetic process
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. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesAcinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2636
Polymers52,8942
Non-polymers3684
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-13 kcal/mol
Surface area19610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.515, 82.065, 83.806
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 26447.102 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii ATCC 19606 = CIP 70.34 = JCM 6841 (bacteria)
Gene: ispD, HMPREF0010_00438 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: D0C6Q8, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES (pH 6.0), 14% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 65831 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Χ2: 0.974 / Net I/σ(I): 6.9 / Num. measured all: 829532
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.6-1.639.31.44832530.6210.8750.4951.5320.9100
1.63-1.66111.30632350.7370.9210.4061.3690.906100
1.66-1.6912.61.23432380.7820.9370.3571.2860.915100
1.69-1.7212.51.02132620.8430.9560.2981.0640.923100
1.72-1.7613.20.87332260.8940.9720.2470.9080.943100
1.76-1.813.40.68132690.9290.9820.1910.7070.951100
1.8-1.8513.20.56132580.9540.9880.1590.5830.96100
1.85-1.912.90.43132630.9690.9920.1240.4490.977100
1.9-1.9512.60.33632660.9790.9950.0980.350.987100
1.95-2.02130.26432760.9870.9970.0750.2750.983100
2.02-2.09130.20532530.9910.9980.0590.2140.991100
2.09-2.1713.30.16632970.9930.9980.0470.1720.967100
2.17-2.2713.10.13332660.9950.9990.0380.1390.953100
2.27-2.3912.40.11132950.9960.9990.0330.1160.934100
2.39-2.5412.90.09632950.9970.9990.0280.10.903100
2.54-2.7413.30.08633030.9970.9990.0240.0890.922100
2.74-3.0113.20.07433130.9970.9990.0210.0770.891100
3.01-3.4512.60.06633520.9980.9990.0190.0690.896100
3.45-4.3412.80.06533740.9970.9990.0190.0680.948100
4.34-5011.70.0935370.9960.9990.0270.0941.62299.8

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
xia2data scaling
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→41.9 Å / Cross valid method: FREE R-VALUE / σ(F): 45.18 / Phase error: 22.07 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2284 3275 5.06 %
Rwork0.21 --
obs0.2116 64741 98.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3533 0 24 522 4079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0133608
X-RAY DIFFRACTIONf_angle_d2.4984893
X-RAY DIFFRACTIONf_dihedral_angle_d10.855480
X-RAY DIFFRACTIONf_chiral_restr0.171587
X-RAY DIFFRACTIONf_plane_restr0.011621
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.27731340.28252274X-RAY DIFFRACTION70
1.63-1.660.26351730.27062912X-RAY DIFFRACTION90
1.66-1.690.31391450.25993061X-RAY DIFFRACTION95
1.69-1.720.2271630.25243099X-RAY DIFFRACTION95
1.72-1.760.27521580.2493063X-RAY DIFFRACTION95
1.76-1.80.24111440.23823124X-RAY DIFFRACTION96
1.8-1.850.24481680.23253090X-RAY DIFFRACTION95
1.85-1.90.25421570.23043101X-RAY DIFFRACTION95
1.9-1.950.24341590.23193111X-RAY DIFFRACTION95
1.95-2.010.25651510.22563122X-RAY DIFFRACTION95
2.01-2.090.24091740.22623086X-RAY DIFFRACTION95
2.09-2.170.23061510.22283138X-RAY DIFFRACTION95
2.17-2.270.21451380.21313130X-RAY DIFFRACTION96
2.27-2.390.22191650.2133120X-RAY DIFFRACTION95
2.39-2.540.25421590.21713137X-RAY DIFFRACTION95
2.54-2.730.24251710.21413127X-RAY DIFFRACTION95
2.73-3.010.21631630.20793159X-RAY DIFFRACTION95
3.01-3.440.19241610.18683184X-RAY DIFFRACTION95
3.45-4.340.19331740.16243193X-RAY DIFFRACTION95
4.34-41.90.22762090.19553293X-RAY DIFFRACTION94

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