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- PDB-7uk8: Apo form of YgiC from Escherichia coli K-12 -

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Basic information

Entry
Database: PDB / ID: 7uk8
TitleApo form of YgiC from Escherichia coli K-12
ComponentsPutative acid--amine ligase YgiC
KeywordsLIGASE / ATP-grasp
Function / homology
Function and homology information


Ligases; Forming carbon-nitrogen bonds; Acid-ammonia (or amine) ligases (amide synthases) / ligase activity / ATP binding / metal ion binding
Similarity search - Function
Glutathionylspermidine synthase, pre-ATP-grasp-like domain / : / Glutathionylspermidine synthase preATP-grasp / Pre-ATP-grasp domain superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Putative acid--amine ligase YgiC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 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 YgiC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,84210
Polymers46,0871
Non-polymers7559
Water4,432246
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.220, 88.220, 141.598
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-644-

HOH

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Components

#1: Protein Putative acid--amine ligase YgiC


Mass: 46086.930 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: ygiC, b3038, JW3006 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P0ADT5, Ligases; Forming carbon-nitrogen bonds; Acid-ammonia (or amine) ligases (amide synthases)
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 3.45 Å3/Da / Density % sol: 64.36 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 1.6 M magnesium sulfate and 100 mM MES pH 6.5

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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: Apr 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.85→38.2 Å / Num. obs: 54990 / % possible obs: 99.8 % / Redundancy: 20.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rpim(I) all: 0.022 / Rrim(I) all: 0.097 / Net I/σ(I): 16.9 / Num. measured all: 1121209 / Scaling rejects: 1
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
1.85-1.8920.12.7356546132570.5070.622.8051.497.4
9.07-38.218.70.062101645430.9990.0140.06346.298.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PHENIX1.18.2-3874refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7UK6

7uk6


Resolution: 1.85→38.2 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2111 2756 5.02 %
Rwork0.1856 52178 -
obs0.1868 54934 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.75 Å2 / Biso mean: 45.5763 Å2 / Biso min: 26.28 Å2
Refinement stepCycle: final / Resolution: 1.85→38.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3137 0 37 246 3420
Biso mean--59.04 49.48 -
Num. residues----383
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.880.30411280.28532522265097
1.88-1.920.30781290.277525972726100
1.92-1.950.27541410.265725312672100
1.95-1.990.28541730.246125512724100
1.99-2.040.24941220.236226132735100
2.04-2.080.2411340.227425932727100
2.08-2.140.27061430.22425622705100
2.14-2.190.26231470.210925752722100
2.19-2.260.28391370.207925942731100
2.26-2.330.27781300.201625912721100
2.33-2.410.21151240.198726042728100
2.41-2.510.20681470.18926002747100
2.51-2.630.22751340.209526052739100
2.63-2.760.21621180.195126282746100
2.76-2.940.2121620.213426132775100
2.94-3.160.27091370.215726032740100
3.16-3.480.21141340.188926462780100
3.48-3.990.18561610.155326192780100
3.99-5.020.15781350.141226882823100
5.02-38.20.19621200.180928432963100

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