[English] 日本語
Yorodumi
- PDB-6ari: Crystal structure of a dephospho-CoA kinase from Escherichia coli... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ari
TitleCrystal structure of a dephospho-CoA kinase from Escherichia coli in complex with inhibitor CM078
ComponentsDephospho-CoA kinase
KeywordsTransferase/Transferase Inhibitor / SSGCID / dephospho-CoA kinase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


dephospho-CoA kinase / dephospho-CoA kinase activity / coenzyme A biosynthetic process / phosphorylation / ATP binding / cytoplasm
Similarity search - Function
Dephospho-CoA kinase / Dephospho-CoA kinase / Dephospho-CoA kinase (DPCK) domain profile. / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BQV / CITRIC ACID / Dephospho-CoA kinase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a dephospho-CoA kinase from Escherichia coli in complex with inhibitor CM078
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionAug 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dephospho-CoA kinase
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,77714
Polymers47,2412
Non-polymers1,53612
Water5,441302
1
A: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3897
Polymers23,6211
Non-polymers7686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dephospho-CoA kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3897
Polymers23,6211
Non-polymers7686
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.720, 63.720, 221.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Dephospho-CoA kinase / / Dephosphocoenzyme A kinase


Mass: 23620.672 Da / Num. of mol.: 2 / Fragment: EscoA.00139.a.JV1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: coaE, yacE, b0103, JW0100 / Plasmid: EscoA.00139.a.JV1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A6I9, dephospho-CoA kinase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-BQV / N-(methylsulfonyl)-3-{[(thiophen-2-yl)sulfanyl]methyl}benzamide


Mass: 327.442 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H13NO3S3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 302 / 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: 2.75 Å3/Da / Density % sol: 55.2 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG_A3_Opt A11 (288528a11): 190 mM ammonium citrate dibasic, 21.23% (w/v) PEG3350: EscoA.00139.a.JV1 at 12mg/mL: bsi107694 10mM o/n soak: 20% eg: iku6-6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 24, 2017
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 36249 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.477 % / Biso Wilson estimate: 26.09 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.092 / Χ2: 1.009 / Net I/σ(I): 16.49
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.058.6150.5913.9526170.9280.62899.9
2.05-2.118.6280.4435.2525560.9520.47100
2.11-2.178.6230.3576.3625000.970.38100
2.17-2.248.6090.2877.724080.9790.305100
2.24-2.318.5980.2458.7523730.9830.261100
2.31-2.398.6450.20910.0622650.9890.222100
2.39-2.488.5970.17611.6922300.9880.188100
2.48-2.588.5820.15712.9721310.990.167100
2.58-2.78.5790.13414.7320370.9930.142100
2.7-2.838.5490.11516.8119640.9940.122100
2.83-2.988.5320.09519.9318940.9960.101100
2.98-3.168.4980.08122.7817590.9970.08699.9
3.16-3.388.4270.0726.1316870.9970.074100
3.38-3.658.3560.05929.3915660.9980.063100
3.65-48.3070.05331.9714500.9980.05699.9
4-4.478.2570.04933.9413160.9980.053100
4.47-5.168.1570.04735.611740.9980.0599.9
5.16-6.328.030.0532.6710280.9980.05499.8
6.32-8.947.7590.04534.428080.9990.048100
8.94-44.1716.7260.0435.194860.9980.04498.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX(1.12rc0_2798: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4i1u

4i1u


Resolution: 2→44.171 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.92
RfactorNum. reflection% reflection
Rfree0.2083 1948 5.38 %
Rwork0.1665 --
obs0.1687 36241 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.17 Å2 / Biso mean: 33.625 Å2 / Biso min: 12.65 Å2
Refinement stepCycle: final / Resolution: 2→44.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3002 0 118 305 3425
Biso mean--60.87 41.38 -
Num. residues----403
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063214
X-RAY DIFFRACTIONf_angle_d0.7594401
X-RAY DIFFRACTIONf_chiral_restr0.049517
X-RAY DIFFRACTIONf_plane_restr0.004582
X-RAY DIFFRACTIONf_dihedral_angle_d14.8971910
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2-2.050.26791120.198724062518
2.05-2.10540.20661510.173923802531
2.1054-2.16740.23531490.16924012550
2.1674-2.23740.21971460.161923742520
2.2374-2.31730.22621330.165524402573
2.3173-2.41010.20831280.161524292557
2.4101-2.51980.19181360.167224392575
2.5198-2.65260.25031320.173324432575
2.6526-2.81880.25561370.179924132550
2.8188-3.03640.27271470.17624612608
3.0364-3.34180.20011370.175224692606
3.3418-3.82520.18331740.15824222596
3.8252-4.81830.18051400.141925302670
4.8183-44.18220.18341260.176426862812
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)
14.80730.68441.32284.11840.08574.8066-0.13810.11870.3229-0.09230.00090.1301-0.14050.12420.12360.22310.0435-0.04520.16830.00750.1711-26.28912.9522-32.907
22.5473-2.51972.06582.6439-1.76482.03460.0715-0.4301-0.12060.3806-0.04680.1138-0.1717-0.4145-0.10890.2432-0.0138-0.01060.22910.02030.1626-33.8588.5328-42.3192
35.4194-1.5813-2.20922.6286-1.24893.7254-0.26450.4003-0.6422-0.0439-0.05740.52060.5946-0.47950.28990.2619-0.05420.02050.2258-0.07830.262-45.60325.6882-55.608
46.89083.61895.14595.0932.83777.4956-0.0470.321-0.1832-0.06880.029-0.2202-0.06010.52450.0310.19010.06610.01050.18920.0250.1614-30.44888.4116-53.2631
52.57290.68340.16783.4184-2.60384.0675-0.24990.5366-0.0208-0.61680.1870.11410.21210.23340.07190.2943-0.003-0.03650.2991-0.01640.1859-24.2663-0.4514-39.4251
62.3195-0.19381.60547.6980.70597.29570.3131-0.45140.28530.02150.07570.8740.1639-1.0102-0.36160.2564-0.0159-0.03930.38480.02850.3868-41.5743-9.4352-30.7546
76.69422.34841.88943.63880.05162.93630.03920.3112-0.6229-0.4980.13950.19730.6455-0.2123-0.14670.4616-0.0001-0.09560.2346-0.04590.3155-33.4299-11.175-36.2838
82.67522.84091.05335.7293-0.20574.8884-0.0846-0.0654-0.06110.1892-0.0365-0.32910.16620.3930.22720.25660.0403-0.04990.2961-0.00740.2178-17.22521.6004-27.4959
92.1138-0.275-1.07892.39881.40964.3383-0.1146-0.0061-0.31330.0529-0.09410.42380.3064-0.14890.18840.1684-0.0583-0.00990.10350.00710.1728-27.008410.5498-6.8288
101.7411-0.56260.5783.8448-3.44793.1611-0.1101-0.125-0.08070.13590.1082-0.1622-0.1511-0.05260.00560.2046-0.0375-0.0310.1623-0.02460.1817-24.8397-4.33319.4937
113.7823.67522.59933.69962.51272.3596-0.29-0.82311.02550.5361-0.0130.0703-0.2896-0.19130.26120.3953-0.0385-0.12740.3585-0.10750.3341-25.8047-1.323121.7179
121.9759-0.25832.31111.0894-0.17768.2388-0.06590.05610.13590.1037-0.0118-0.3051-0.2780.81340.02340.1963-0.0784-0.0380.19270.03150.2769-16.5874-2.54077.15
131.7512-1.9014-1.86924.08381.37942.4619-0.1444-0.29850.16150.4350.1857-0.24560.26810.3718-0.00950.2189-0.0344-0.04490.2058-0.00940.1735-20.086611.3224-3.5328
144.2275-0.8801-3.76990.94250.18935.3068-0.1385-0.1278-0.20720.04410.0951-0.06220.1613-0.02080.02890.162-0.0395-0.00890.1167-0.00410.1358-28.905522.08658.2425
152.8057-1.8858-1.32633.27552.42125.10260.01490.2145-0.1062-0.094-0.05950.1638-0.00240.09430.02220.1759-0.0696-0.00580.1290.01130.1535-23.599515.357-14
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )A1 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 40 )A28 - 40
3X-RAY DIFFRACTION3chain 'A' and (resid 41 through 77 )A41 - 77
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 102 )A78 - 102
5X-RAY DIFFRACTION5chain 'A' and (resid 103 through 133 )A103 - 133
6X-RAY DIFFRACTION6chain 'A' and (resid 134 through 145 )A134 - 145
7X-RAY DIFFRACTION7chain 'A' and (resid 146 through 178 )A146 - 178
8X-RAY DIFFRACTION8chain 'A' and (resid 179 through 200 )A179 - 200
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 27 )B1 - 27
10X-RAY DIFFRACTION10chain 'B' and (resid 28 through 54 )B28 - 54
11X-RAY DIFFRACTION11chain 'B' and (resid 55 through 77 )B55 - 77
12X-RAY DIFFRACTION12chain 'B' and (resid 78 through 102 )B78 - 102
13X-RAY DIFFRACTION13chain 'B' and (resid 103 through 133 )B103 - 133
14X-RAY DIFFRACTION14chain 'B' and (resid 134 through 168 )B134 - 168
15X-RAY DIFFRACTION15chain 'B' and (resid 169 through 203 )B169 - 203

+
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