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- PDB-7uka: YgiC from Escherichia coli K-12 in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 7uka
TitleYgiC from Escherichia coli K-12 in complex with ADP
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
ADENOSINE-5'-DIPHOSPHATE / NICKEL (II) ION / Putative acid--amine ligase YgiC
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)47,1499
Polymers46,0871
Non-polymers1,0628
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.131, 88.131, 139.909
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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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-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-NI / NICKEL (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.4 Å3/Da / Density % sol: 63.86 %
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: Jun 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→44.07 Å / Num. obs: 32581 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 1 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.015 / Rrim(I) all: 0.069 / Net I/σ(I): 25.9 / Num. measured all: 666547
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
2.2-2.2720.82.4685759127690.5970.5492.5291.4100
9.07-44.0718.50.03992853610.0070.03192.199.2

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Processing

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

7uk6


Resolution: 2.2→39.8 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1591 4.89 %
Rwork0.2178 30939 -
obs0.2196 32530 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.9 Å2 / Biso mean: 62.8571 Å2 / Biso min: 39.72 Å2
Refinement stepCycle: final / Resolution: 2.2→39.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2923 0 58 32 3013
Biso mean--74.95 60.03 -
Num. residues----368
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.270.28771630.282327122875
2.27-2.350.29041550.251827692924
2.35-2.450.31921280.252828102938
2.45-2.560.31251470.255127472894
2.56-2.690.30371470.258227972944
2.69-2.860.28481350.257327872922
2.86-3.080.31571570.254927812938
3.08-3.390.27741370.2428502987
3.39-3.880.23131530.206728082961
3.88-4.890.19071150.186728943009
4.89-39.80.26541540.209929843138

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