[English] 日本語
Yorodumi
- PDB-9gqv: Pseudomonas aeruginosa FabF C164A in complex with N-((1-((2-hydro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9gqv
TitlePseudomonas aeruginosa FabF C164A in complex with N-((1-((2-hydroxy-4-methylpentanamido)methyl)cyclobutyl)methyl)-1H-pyrazole-3-carboxamide
Components3-oxoacyl-[acyl-carrier-protein] synthase 2
KeywordsTRANSFERASE / inhibitor / protein-ligand complex / FabF
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase II / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / metal ion binding / cytosol
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Beta-ketoacyl synthase / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like
Similarity search - Domain/homology
: / FORMIC ACID / 3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.766 Å
AuthorsYadrykhins'ky, V. / Brenk, R.
Funding support Norway, 2items
OrganizationGrant numberCountry
Other governmentF-12602
Research Council of Norway273588 Norway
CitationJournal: Eur.J.Med.Chem. / Year: 2025
Title: Towards new antibiotics: P. aeruginosa FabF ligands discovered by crystallographic fragment screening followed by hit expansion.
Authors: Georgiou, C. / Espeland, L.O. / Bukya, H. / Yadrykhins'ky, V. / Haug, B.E. / Mainkar, P.S. / Brenk, R.
History
DepositionSep 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,98928
Polymers87,9932
Non-polymers1,99626
Water6,215345
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,95714
Polymers43,9961
Non-polymers96013
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,03214
Polymers43,9961
Non-polymers1,03513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.679, 103.811, 143.318
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: ALA / End label comp-ID: ALA / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 4 - 413 / Label seq-ID: 9 - 418

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 2


Mass: 43996.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: fabF1, PA2965 / Production host: Escherichia coli (E. coli)
References: UniProt: G3XDA2, beta-ketoacyl-[acyl-carrier-protein] synthase II

-
Non-polymers , 5 types, 371 molecules

#2: Chemical ChemComp-A1IOR / ~{N}-[[1-[[[(2~{S})-4-methyl-2-oxidanyl-pentanoyl]amino]methyl]cyclobutyl]methyl]-1~{H}-pyrazole-3-carboxamide


Mass: 322.403 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H26N4O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.24M ammonium formate and 35% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8731 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 15, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 1.766→51.91 Å / Num. obs: 73113 / % possible obs: 99.21 % / Redundancy: 4.6 % / CC1/2: 0.989 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.053 / Rrim(I) all: 0.113 / Net I/av σ(I): 10 / Net I/σ(I): 8.1
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 4.3 % / Rmerge(I) obs: 1.276 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 3398 / CC1/2: 0.28 / Rpim(I) all: 0.713 / Rrim(I) all: 1.471 / % possible all: 93.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia23.12.0data reduction
DIALS3.12.1data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.766→51.905 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.159 / SU ML: 0.117 / Cross valid method: FREE R-VALUE / ESU R: 0.128 / ESU R Free: 0.123
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2222 3737 5.113 %
Rwork0.1818 69350 -
all0.184 --
obs-73087 99.151 %
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.684 Å2
Baniso -1Baniso -2Baniso -3
1--0.689 Å2-0 Å2-0 Å2
2--1.325 Å2-0 Å2
3----0.637 Å2
Refinement stepCycle: LAST / Resolution: 1.766→51.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6032 0 124 345 6501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0126308
X-RAY DIFFRACTIONr_bond_other_d0.0050.0165956
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.8048521
X-RAY DIFFRACTIONr_angle_other_deg1.0351.73713644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3715844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.275.93864
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.78754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06610964
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.77210263
X-RAY DIFFRACTIONr_chiral_restr0.1140.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.010.027737
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021493
X-RAY DIFFRACTIONr_nbd_refined0.1790.21149
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1450.25458
X-RAY DIFFRACTIONr_nbtor_refined0.1470.23031
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0660.23313
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1070.2382
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0550.220
X-RAY DIFFRACTIONr_nbd_other0.1140.2236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1010.231
X-RAY DIFFRACTIONr_mcbond_it2.7082.3423310
X-RAY DIFFRACTIONr_mcbond_other2.7072.3433311
X-RAY DIFFRACTIONr_mcangle_it3.3854.2174143
X-RAY DIFFRACTIONr_mcangle_other3.3854.2194144
X-RAY DIFFRACTIONr_scbond_it4.1142.9022998
X-RAY DIFFRACTIONr_scbond_other4.1142.9032999
X-RAY DIFFRACTIONr_scangle_it5.8385.1044363
X-RAY DIFFRACTIONr_scangle_other5.8385.1044364
X-RAY DIFFRACTIONr_lrange_it6.90524.1466771
X-RAY DIFFRACTIONr_lrange_other6.86224.0266711
X-RAY DIFFRACTIONr_ncsr_local_group_10.0560.0513040
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.056360.05008
12AX-RAY DIFFRACTIONLocal ncs0.056360.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.766-1.8120.3422360.33148780.33253720.9020.90495.19730.321
1.812-1.8610.2982890.30549810.30552810.9210.92199.79170.289
1.861-1.9150.2792840.27747930.27750780.940.94299.98030.253
1.915-1.9740.2382340.24847370.24849720.9580.95699.97990.219
1.974-2.0390.2412320.22845890.22848250.9580.96499.91710.19
2.039-2.110.2532630.21244130.21446770.9570.96999.97860.171
2.11-2.190.2342580.18742740.1945360.9650.97799.91180.15
2.19-2.2790.2292300.17640890.17943230.9630.9899.90750.136
2.279-2.380.2031950.1739490.17241570.9740.98299.68730.132
2.38-2.4960.2421970.16837900.17240120.9590.98399.37690.131
2.496-2.6310.2032090.16434680.16737820.9750.98497.22370.131
2.631-2.790.1941730.15434390.15636310.9770.98699.47670.122
2.79-2.9820.1891390.15132400.15233820.9760.98699.91130.124
2.982-3.220.2421470.17429980.17731520.9630.9899.77790.149
3.22-3.5260.1881510.15227670.15429310.9790.98699.55650.136
3.526-3.9390.2121250.16325170.16526560.9750.98599.47290.152
3.939-4.5450.1751450.14922190.1523840.9810.98699.16110.145
4.545-5.5550.209980.16818650.1720120.9770.98497.56460.165
5.555-7.8120.227760.214750.20115800.9640.97498.16460.192
7.812-51.9050.306560.2178690.2239480.9170.95697.57380.225
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)
11.0057-0.0518-0.4990.00470.02120.2588-0.0399-0.09880.0346-0.00190.0129-0.01720.03530.05670.0270.01490.01720.02690.0481-0.00710.1364-35.8904-3.612432.249
20.20120.08190.07280.37110.26510.2163-0.00460.0078-0.07110.03130.018-0.03810.0182-0.0157-0.01350.02110.00020.00640.03490.00830.1404-5.2089-14.251468.2456
Refinement TLS groupSelection: 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