[English] 日本語
Yorodumi
- PDB-6rgb: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rgb
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complexe with an inhibitor
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
Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / 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 / Tumour Suppressor Smad4 / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Chem-K38 / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes EGD-e (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsGelin, M. / Labesse, G.
CitationJournal: Acs Infect Dis. / Year: 2020
Title: From Substrate to Fragments to Inhibitor ActiveIn VivoagainstStaphylococcus aureus.
Authors: Gelin, M. / Paoletti, J. / Nahori, M.A. / Huteau, V. / Leseigneur, C. / Jouvion, G. / Dugue, L. / Clement, D. / Pons, J.L. / Assairi, L. / Pochet, S. / Labesse, G. / Dussurget, O.
History
DepositionApr 16, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2May 15, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8073
Polymers31,0451
Non-polymers7622
Water1,65792
1
A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules

A: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,22812
Polymers124,1814
Non-polymers3,0478
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)62.790, 75.620, 118.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22

-
Components

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


Mass: 31045.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes EGD-e (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-K38 / (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[[3-[6-azanyl-9-[(2~{R},3~{R},4~{S},5~{R})-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]purin-8-yl]prop-2-ynylamino]methyl]oxolane-3,4-diol


Mass: 569.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27N11O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.53 % / Mosaicity: 0.92 °
Crystal growTemperature: 291.15 K / Method: evaporation / pH: 5
Details: 30 mM NaBr, 220 mM Kcitrate, glycerol 6%, 15-16% w/v PEG400

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.25→37.81 Å / Num. obs: 13690 / % possible obs: 99.5 % / Redundancy: 5.4 % / Biso Wilson estimate: 30.39 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Net I/σ(I): 16.4 / Num. measured all: 74351 / Scaling rejects: 233
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
2.25-2.324.90.48598412120.790.2540.5483.597.9
8.98-37.814.60.02911302450.9990.0140.03341.197.3

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
MOSFLMdata reduction
Aimless0.7.2data scaling
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→37.39 Å / SU ML: 0.2467 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.142 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2306 694 5.09 %
Rwork0.2062 12932 -
obs0.2075 13626 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.71 Å2
Refinement stepCycle: LAST / Resolution: 2.25→37.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2075 0 54 92 2221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00832226
X-RAY DIFFRACTIONf_angle_d0.6893022
X-RAY DIFFRACTIONf_chiral_restr0.0551326
X-RAY DIFFRACTIONf_plane_restr0.0034383
X-RAY DIFFRACTIONf_dihedral_angle_d20.20731311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.420.32891330.27752472X-RAY DIFFRACTION96.41
2.42-2.660.2671330.23682577X-RAY DIFFRACTION99.34
2.66-3.050.23171450.23092566X-RAY DIFFRACTION99.45
3.05-3.840.20611320.19692621X-RAY DIFFRACTION99.71
3.84-37.40.21671510.17792696X-RAY DIFFRACTION99.13
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.339966236230.0328871141332-1.245357486530.9638701981980.3369585530455.51025794755-0.0465661703928-0.3508546970430.2057402734040.1461113753950.001583162106160.0800892521621-0.422530736306-0.218290785537-0.02169243919240.3824927754080.1205948884380.01545114415730.407683368197-0.1050754715070.27118115638410.120635406924.707764995822.1197048992
23.79441493299-0.00529631052913-1.604071644540.0751177535862-0.09087637933856.12575294563-0.340872671619-0.980371670670.5278994732310.2519450422630.626499807244-0.4818008887730.3190686997930.9429517649640.02616554289880.4313808364180.1702598939430.02917439502860.699398606707-0.1238220351570.44361017052520.550793985221.117209744726.3268912812
32.187017823350.358251785264-0.4026300720461.738373840960.293202789133.326683876080.01161865672070.03140097801630.220886046488-0.0268180649952-0.1092231986960.315232187064-0.400446178687-0.5896406644020.1629897184670.2045573053450.08708201933690.002974460511680.3268651485710.02140267497750.30055168241114.704312794918.2407359353-1.08660006621
41.816970223160.0947135552730.3419632026481.604319861420.9991726303983.625247538930.002692419250240.07243888105110.0280588855725-0.1405431175123.17819052678E-50.128431558279-0.185405493116-0.1030612792760.0275493846850.1531809716280.02620178330130.004386655733560.146997537232-0.000773165234360.18377153586923.255331872911.8383081274-1.98931347112
51.65556826655-0.214873615525-0.3778956219021.816155729140.3749954019583.123656694420.07667555997190.1115384363350.0771604597387-0.00293180070056-0.1488774581580.28513571006-0.0718082217493-0.4110676406650.08238597751520.2114112178210.045802059433-0.005474955581470.2533583141660.01715456294860.27533040880517.311537252514.4931228822-2.89682967908
65.008915568180.705021859365-0.3756743922144.786034100142.002551866525.335048117420.0305002481505-0.988441819182-0.09958956255170.9091188410270.276377314847-0.1286732916120.4092319559640.122228469458-0.02900280408160.2716506848920.03169111680790.04495550261070.327086925642-0.02875433994880.21890030893131.503089192512.825836861217.5076182638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 68 )
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 92 )
3X-RAY DIFFRACTION3chain 'A' and (resid 93 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 184 )
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 252 )
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 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