[English] 日本語
Yorodumi
- PDB-7krk: Putative FabG from Acinetobacter baumannii -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7krk
TitlePutative FabG from Acinetobacter baumannii
Components3-oxoacyl-[acyl-carrier-protein] reductase
KeywordsOXIDOREDUCTASE / FabG / Acinetobacter baumannii / enzyme
Function / homology
Function and homology information


glucose 1-dehydrogenase [NAD(P)+] activity / glucose 1-dehydrogenase [NAD(P)+] / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / nucleotide binding
Similarity search - Function
: / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShaw, K.I. / Smith, K.M. / Cross, E.M.
CitationJournal: To Be Published
Title: Putative FabG from Acinetobacter baumannii
Authors: Forwood, J.K.
History
DepositionNov 20, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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: 3-oxoacyl-[acyl-carrier-protein] reductase
B: 3-oxoacyl-[acyl-carrier-protein] reductase
C: 3-oxoacyl-[acyl-carrier-protein] reductase
D: 3-oxoacyl-[acyl-carrier-protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6316
Polymers103,4464
Non-polymers1842
Water16,772931
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13770 Å2
ΔGint-58 kcal/mol
Surface area32080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.522, 189.522, 71.382
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Space group name HallR3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

-
Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase FabG / Glucose 1-dehydrogenase / SDR family oxidoreductase


Mass: 25861.596 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: fabG_1, ABC003_00909, ABUW_2930, DLI69_07500, EA686_12865, FDO31_05475, GNY86_08660
Production host: Escherichia coli (E. coli)
References: UniProt: A0A077GFB1, glucose 1-dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 931 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.43 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 0.2 M ammonium tartrate dibasic, pH 6.6, 20% v/v PEG3350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.4→29.82 Å / Num. obs: 188133 / % possible obs: 99.9 % / Redundancy: 9.9 % / Biso Wilson estimate: 11.82 Å2 / CC1/2: 0.998 / Net I/σ(I): 13.5
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 9178 / CC1/2: 0.761

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
Aimlessdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I01

1i01


Resolution: 1.4→29.82 Å / SU ML: 0.1048 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 13.9256 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1568 9533 5.07 %
Rwork0.1452 178596 -
obs0.1458 188129 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.17 Å2
Refinement stepCycle: LAST / Resolution: 1.4→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6954 0 12 931 7897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027061
X-RAY DIFFRACTIONf_angle_d0.47419532
X-RAY DIFFRACTIONf_chiral_restr0.05441129
X-RAY DIFFRACTIONf_plane_restr0.00331257
X-RAY DIFFRACTIONf_dihedral_angle_d13.75732579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.420.20963230.21855795X-RAY DIFFRACTION97.33
1.42-1.430.22142630.20926010X-RAY DIFFRACTION99.92
1.43-1.450.2043030.19815953X-RAY DIFFRACTION100
1.45-1.470.19943140.1785962X-RAY DIFFRACTION100
1.47-1.490.17493620.17685916X-RAY DIFFRACTION100
1.49-1.510.19253110.16995956X-RAY DIFFRACTION100
1.51-1.530.1873080.16435991X-RAY DIFFRACTION100
1.53-1.550.17573260.15835968X-RAY DIFFRACTION99.98
1.55-1.580.16823340.15945934X-RAY DIFFRACTION100
1.58-1.60.18093370.15875930X-RAY DIFFRACTION100
1.6-1.630.17853330.15245954X-RAY DIFFRACTION100
1.63-1.660.16373450.15585944X-RAY DIFFRACTION100
1.66-1.690.18193510.14985891X-RAY DIFFRACTION100
1.69-1.730.14943350.14335968X-RAY DIFFRACTION100
1.73-1.760.14723000.1395916X-RAY DIFFRACTION100
1.76-1.80.15993370.13625982X-RAY DIFFRACTION100
1.8-1.850.14623240.13325893X-RAY DIFFRACTION100
1.85-1.90.15282950.13746043X-RAY DIFFRACTION100
1.9-1.960.15883610.13425915X-RAY DIFFRACTION100
1.96-2.020.14632930.13025988X-RAY DIFFRACTION100
2.02-2.090.14242750.13196022X-RAY DIFFRACTION100
2.09-2.170.13923340.13075906X-RAY DIFFRACTION100
2.17-2.270.13212600.12546014X-RAY DIFFRACTION100
2.27-2.390.14062800.12526016X-RAY DIFFRACTION100
2.39-2.540.1473020.13045993X-RAY DIFFRACTION100
2.54-2.740.14812940.14165981X-RAY DIFFRACTION100
2.74-3.020.15533480.14265922X-RAY DIFFRACTION100
3.02-3.450.1423770.14575889X-RAY DIFFRACTION100
3.45-4.350.15313090.13265954X-RAY DIFFRACTION100
4.35-29.820.16982990.17165990X-RAY DIFFRACTION99.95

+
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