[English] 日本語
Yorodumi
- PDB-8ckh: Crystal structure of IspE from Klebsiella pneumoniae -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ckh
TitleCrystal structure of IspE from Klebsiella pneumoniae
Components4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
KeywordsPROTEIN BINDING / 4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL KINASE / IspE / Klebsiella pneumoniae.
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionFeb 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 28, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)62,7254
Polymers61,7122
Non-polymers1,0122
Water5,332296
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-17 kcal/mol
Surface area22150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.870, 76.781, 98.517
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

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


Mass: 30856.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: ispE, ipk, B5L96_11675, BN49_3345, FXN67_13605, GNE24_13115, GNG14_12250, NCTC13465_02970, NCTC13635_07143, NCTC5052_02044, NCTC9140_05240, NCTC9601_01067, NCTC9661_03960, SAMEA3499874_01580, ...Gene: ispE, ipk, B5L96_11675, BN49_3345, FXN67_13605, GNE24_13115, GNG14_12250, NCTC13465_02970, NCTC13635_07143, NCTC5052_02044, NCTC9140_05240, NCTC9601_01067, NCTC9661_03960, SAMEA3499874_01580, SAMEA3499901_04677, SAMEA3538828_04749
Production host: Escherichia coli (E. coli)
References: UniProt: W9BPL2, 4-(cytidine 5'-diphospho)-2-C-methyl-D-erythritol kinase
#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 100 mM HEPES pH7.0 1 M Sodium citrate / PH range: 7.0-7.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.0007 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0007 Å / Relative weight: 1
ReflectionResolution: 1.8→44.58 Å / Num. obs: 46367 / % possible obs: 98.53 % / Redundancy: 6.3 % / Biso Wilson estimate: 26.99 Å2 / Rmerge(I) obs: 0.079 / Rrim(I) all: 0.087 / Net I/σ(I): 11
Reflection shellResolution: 1.8→1.8 Å / Num. unique obs: 4526 / Rrim(I) all: 0.695 / % possible all: 97.41

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487phasing
PHENIX1.20.1_4487refinement
Aimless1.20.1_4487data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→44.58 Å / SU ML: 0.1856 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.4377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2267 2000 4.32 %
Rwork0.1884 44336 -
obs0.19 46336 98.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.45 Å2
Refinement stepCycle: LAST / Resolution: 1.8→44.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4275 0 62 296 4633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00484440
X-RAY DIFFRACTIONf_angle_d0.79556069
X-RAY DIFFRACTIONf_chiral_restr0.0492685
X-RAY DIFFRACTIONf_plane_restr0.0098787
X-RAY DIFFRACTIONf_dihedral_angle_d10.2256613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.850.28151400.2343108X-RAY DIFFRACTION98.04
1.85-1.890.31111390.233065X-RAY DIFFRACTION97.06
1.89-1.950.2321410.22663140X-RAY DIFFRACTION99.09
1.95-2.010.26831440.20233175X-RAY DIFFRACTION99.37
2.01-2.090.2681410.19843141X-RAY DIFFRACTION99.18
2.09-2.170.2471420.1943137X-RAY DIFFRACTION99.27
2.17-2.270.26821430.20063176X-RAY DIFFRACTION99.37
2.27-2.390.24541440.20193184X-RAY DIFFRACTION99.64
2.39-2.540.23221420.1993157X-RAY DIFFRACTION98.45
2.54-2.730.23461410.19423135X-RAY DIFFRACTION97.36
2.73-3.010.23571440.19423197X-RAY DIFFRACTION99.79
3.01-3.440.21031460.18643225X-RAY DIFFRACTION99.32
3.44-4.340.20821450.16013232X-RAY DIFFRACTION98.63
4.34-44.580.20041480.1833264X-RAY DIFFRACTION95.31
Refinement TLS params.Method: refined / Origin x: 39.1260751016 Å / Origin y: 24.3356078802 Å / Origin z: 73.5618338654 Å
111213212223313233
T0.193084758536 Å20.00247546626507 Å2-0.00734482685061 Å2-0.139104989724 Å2-0.0139812774181 Å2--0.184170407087 Å2
L1.06721199807 °2-0.0774683028385 °20.210332521432 °2-0.19572742965 °2-0.0143925032354 °2--0.496196905122 °2
S0.0486505709904 Å °0.0289453578892 Å °-0.0254863002552 Å °0.0303558812964 Å °-0.0843066222218 Å °0.00591774292799 Å °-0.00579103890087 Å °-0.00273582505241 Å °-0.00229461070272 Å °
Refinement TLS groupSelection details: all

+
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