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- PDB-7uk7: YjfC from Escherichia coli K-12 in complex with ADP, Mg2+ and SO4 -

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Basic information

Entry
Database: PDB / ID: 7uk7
TitleYjfC from Escherichia coli K-12 in complex with ADP, Mg2+ and SO4
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 / ADENOSINE-5'-DIPHOSPHATE / Putative acid--amine ligase YjfC
Function and homology information
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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)46,6946
Polymers46,0261
Non-polymers6685
Water7,837435
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.010, 68.885, 114.309
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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.82 Å3/Da / Density % sol: 56.43 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 200 mM lithium sulfate monohydrate, 100 mM Tris-HCl pH 8.5, and 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jul 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.95→43.99 Å / Num. obs: 38719 / % possible obs: 99.9 % / Redundancy: 13.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.029 / Rrim(I) all: 0.107 / Net I/σ(I): 20.1 / Num. measured all: 525889 / Scaling rejects: 3
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
1.95-212.50.8363293426370.8470.2420.8713.298.5
8.94-43.9912.20.026590248210.0080.02772.199.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.1.2-3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UK6

7uk6


Resolution: 1.95→43.99 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 1901 4.92 %
Rwork0.1583 36755 -
obs0.16 38656 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.03 Å2 / Biso mean: 27.708 Å2 / Biso min: 14.51 Å2
Refinement stepCycle: final / Resolution: 1.95→43.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 39 435 3665
Biso mean--20.39 36.24 -
Num. residues----389
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-20.24421240.19482543266798
2-2.050.21071390.176425612700100
2.05-2.110.2121490.167325912740100
2.11-2.180.22581210.166826232744100
2.18-2.260.21261270.151525692696100
2.26-2.350.19231340.152826182752100
2.35-2.460.18851280.155926102738100
2.46-2.590.21561540.163325822736100
2.59-2.750.22131300.165826482778100
2.75-2.960.22341190.174226172736100
2.96-3.260.20811410.177326422783100
3.26-3.730.18861440.154826562800100
3.73-4.70.16131340.1326842818100
4.7-43.990.1531570.157728112968100

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