[English] 日本語
Yorodumi
- PDB-8xkg: Crystal structure of Acinetobacter baumannii IspD -

+
Open data


ID or keywords:

Loading...

-
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
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more