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- PDB-7uk6: Apo form of YjfC from Escherichia coli K-12 -

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Basic information

Entry
Database: PDB / ID: 7uk6
TitleApo form of YjfC from Escherichia coli K-12
ComponentsPutative acid--amine ligase YjfC
KeywordsLIGASE / ATP-grasp
Function / homologyLigases; Forming carbon-nitrogen bonds; Acid-ammonia (or amine) ligases (amide synthases) / Glutathionylspermidine synthase, pre-ATP-grasp-like domain / Glutathionylspermidine synthase preATP-grasp / Pre-ATP-grasp domain superfamily / ligase activity / ATP binding / metal ion binding / Putative acid--amine ligase YjfC
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPederick, J.L. / Bruning, J.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochemistry / Year: 2023
Title: Escherichia coli YgiC and YjfC Possess Peptide─Spermidine Ligase Activity.
Authors: Pederick, J.L. / Klose, J. / Jovcevski, B. / Pukala, T.L. / Bruning, J.B.
History
DepositionMar 31, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative acid--amine ligase YjfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,6027
Polymers46,0261
Non-polymers5766
Water5,206289
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.323, 70.760, 112.041
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative acid--amine ligase YjfC


Mass: 46025.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: yjfC, b4186, JW4144 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P33222, Ligases; Forming carbon-nitrogen bonds; Acid-ammonia (or amine) ligases (amide synthases)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM lithium sulfate monohydrate, 0.1 M Tris-HCl pH 8.5, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 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: Jul 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→44.42 Å / Num. obs: 42317 / % possible obs: 100 % / Redundancy: 13.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.025 / Rrim(I) all: 0.092 / Net I/σ(I): 15.5 / Num. measured all: 559446 / Scaling rejects: 19
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
1.9-1.9413.91.593712526650.7340.4391.651.9100
9.11-44.4211.10.03511446010.0090.03147.599.3

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
XDSdata reduction
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IOB

2iob


Resolution: 1.9→36.62 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1972 2138 5.06 %
Rwork0.1692 40094 -
obs0.1707 42232 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.11 Å2 / Biso mean: 40.7611 Å2 / Biso min: 24.29 Å2
Refinement stepCycle: final / Resolution: 1.9→36.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3184 0 30 289 3503
Biso mean--61.34 47.09 -
Num. residues----389
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.940.32151330.28326202753
1.94-1.990.26111520.231625942746
1.99-2.050.25831230.208526542777
2.05-2.110.28351260.201426762802
2.11-2.170.23921340.199126472781
2.17-2.250.25711200.187826572777
2.25-2.340.24251460.184826522798
2.34-2.450.20381300.17526602790
2.45-2.580.21451580.177726342792
2.58-2.740.21981560.178926682824
2.74-2.950.22031480.183326812829
2.95-3.250.20041740.183226492823
3.25-3.720.17821240.171327312855
3.72-4.680.16411430.133927322875
4.68-36.620.17161710.153628393010

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