[English] 日本語
Yorodumi
- PDB-8b47: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8b47
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a cyclic di-adenosine derivative
ComponentsNAD kinase 1
KeywordsTRANSFERASE / tetrameric NAD-kinase
Function / homology
Function and homology information


NAD+ kinase / NAD+ kinase activity / NADP+ biosynthetic process / NAD+ metabolic process / NAD binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal
Similarity search - Domain/homology
Chem-OWU / PHOSPHATE ION / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsGelin, M. / Labesse, G.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE18-0011-02 France
French Infrastructure for Integrated Structural Biology (FRISBI)ANR-10-INSB-05-01 France
CitationJournal: Eur.J.Med.Chem. / Year: 2023
Title: Synthesis and structure-activity relationship studies of original cyclic diadenosine derivatives as nanomolar inhibitors of NAD kinase from pathogenic bacteria.
Authors: Clement, D.A. / Gelin, M. / Leseigneur, C. / Huteau, V. / Mondange, L. / Pons, J.L. / Dussurget, O. / Lionne, C. / Labesse, G. / Pochet, S.
History
DepositionSep 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD kinase 1
B: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9507
Polymers62,0912
Non-polymers1,8605
Water1,18966
1
A: NAD kinase 1
B: NAD kinase 1
hetero molecules

A: NAD kinase 1
B: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,90014
Polymers124,1814
Non-polymers3,71910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area9770 Å2
ΔGint-84 kcal/mol
Surface area41410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.406, 145.885, 54.904
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein NAD kinase 1 / ATP-dependent NAD kinase


Mass: 31045.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-OWU / (1~{R},23~{R},24~{S},25~{R})-14-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-7-azanyl-24,25-bis(oxidanyl)-20,20-bis(oxidanylidene)-26-oxa-20$l^{6}-thia-2,4,6,9,14,17,21-heptazatetracyclo[21.2.1.0^{2,10}.0^{3,8}]hexacosa-3,5,7,9-tetraen-11-yn-16-one


Mass: 715.698 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N13O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES pH 7.5, 25 %(v/v) PEG 550 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.53→72.94 Å / Num. obs: 17576 / % possible obs: 98.7 % / Redundancy: 12.3 % / Biso Wilson estimate: 59.07 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.218 / Rpim(I) all: 0.063 / Rrim(I) all: 0.227 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.53-2.637.12.1341246117550.3590.8412.3050.889.6
9.1-72.9411.20.06150054480.9990.0180.06433.999.8

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimless0.7.7data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6RG9

6rg9


Resolution: 2.53→51.39 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 3247 10.04 %
Rwork0.2029 29106 -
obs0.2085 17478 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.13 Å2 / Biso mean: 62.511 Å2 / Biso min: 38.54 Å2
Refinement stepCycle: final / Resolution: 2.53→51.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4134 0 148 66 4348
Biso mean--68.07 56.56 -
Num. residues----520
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.53-2.560.32031080.3061933104172
2.56-2.60.30871370.30541185132292
2.6-2.650.38781430.32051256139996
2.65-2.690.36861350.29571206134197
2.69-2.740.36441440.31631279142398
2.74-2.790.45391440.334712991443100
2.79-2.850.35681420.288212801422100
2.85-2.910.32791460.27412821428100
2.91-2.980.30431430.258912951438100
2.98-3.050.29281480.226213191467100
3.05-3.140.2791410.231112721413100
3.14-3.230.30121480.222613051453100
3.23-3.330.26011460.230312811427100
3.33-3.450.28721440.227112901434100
3.45-3.590.24221400.170812781418100
3.59-3.750.21491480.17412831431100
3.75-3.950.27161430.162213111454100
3.95-4.20.20981470.16813211468100
4.2-4.520.21011380.152312671405100
4.52-4.980.17241420.150512871429100
4.98-5.70.29921390.188413041443100
5.7-7.170.28611380.208112841422100
7.18-51.390.22071430.21021289143299
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.0249-0.9277-1.18642.9001-0.41686.22790.1390.1753-0.0387-0.1024-0.0628-0.2006-0.04970.2182-0.08680.3713-0.029-0.04660.42870.0250.428523.073222.0401-6.9716
21.1015-0.1874-0.19120.3008-0.31482.8686-0.08-0.0647-0.01530.06260.0452-0.01290.18580.03740.04540.4433-0.00930.02720.3581-0.00760.551913.973615.51411.8265
36.724-4.36162.04794.8513-4.33345.09970.4485-0.0542-1.18552.7147-0.51430.7246-1.0480.2628-0.06621.0878-0.19980.05850.4862-0.0070.78285.7730.191827.3906
41.9879-0.02310.43771.5282-0.70364.60420.11170.0835-0.0178-0.0026-0.1158-0.2033-0.13950.3435-0.00490.36820.02030.02180.3114-0.00320.49714.719915.496412.198
50.565-0.00970.74391.47051.45068.92650.0226-0.21410.14390.117-0.07610.0891-0.6925-0.53050.08180.38070.04650.0350.4452-0.01640.4788-17.069123.897928.6498
62.83130.09510.70241.8827-0.92053.37180.15070.02790.0416-0.0988-0.0710.0614-0.066-0.1046-0.08210.34550.0550.02910.3187-0.02570.4587-9.336114.397713.7483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 79 )A1 - 79
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 184 )A80 - 184
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 198 )A185 - 198
4X-RAY DIFFRACTION4chain 'A' and (resid 199 through 263 )A199 - 263
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 141 )B1 - 141
6X-RAY DIFFRACTION6chain 'B' and (resid 142 through 264 )B142 - 264

+
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