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- PDB-8vxb: Structure of ANT(6)-Ib from Campylobacter fetus subsp fetus compl... -

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Basic information

Entry
Database: PDB / ID: 8vxb
TitleStructure of ANT(6)-Ib from Campylobacter fetus subsp fetus complexed with hydrated streptomycin
ComponentsStreptomycin aminoglycoside adenylyltransferase ant(6)-Ib
KeywordsTRANSFERASE / Campylobacter / streptomycin / antibiotic resistance
Function / homologyAminoglycoside 6-adenylyltransferase / Streptomycin adenylyltransferase / nucleotidyltransferase activity / Nucleotidyltransferase superfamily / Chem-5I0 / PHOSPHATE ION / Streptomycin aminoglycoside adenylyltransferase ant(6)-Ib
Function and homology information
Biological speciesCampylobacter fetus subsp. fetus (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsNalam, P. / Cook, P. / Smith, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other government United States
CitationJournal: Proteins / Year: 2025
Title: Structural and Biochemical Characterization of Aminoglycoside Nucleotidyltransferase(6)-Ib From Campylobacter fetus subsp. fetus.
Authors: Nalam, P. / Cook, P.D. / Smith, B.A.
History
DepositionFeb 4, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptomycin aminoglycoside adenylyltransferase ant(6)-Ib
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2153
Polymers36,5181
Non-polymers6982
Water5,765320
1
A: Streptomycin aminoglycoside adenylyltransferase ant(6)-Ib
hetero molecules

A: Streptomycin aminoglycoside adenylyltransferase ant(6)-Ib
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,4316
Polymers73,0362
Non-polymers1,3954
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7010 Å2
ΔGint-36 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.305, 73.305, 127.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-589-

HOH

21A-816-

HOH

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Components

#1: Protein Streptomycin aminoglycoside adenylyltransferase ant(6)-Ib


Mass: 36517.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter fetus subsp. fetus (Campylobacter)
Gene: ant(6)-Ib / Production host: Escherichia coli (E. coli) / References: UniProt: D8L9Z0
#2: Chemical ChemComp-5I0 / [(2~{S},3~{S},4~{S},5~{R},6~{S})-2-[(2~{R},3~{R},4~{R},5~{S})-2-[(1~{R},2~{S},3~{R},4~{R},5~{S},6~{R})-2,4-bis[[azaniumylidene(azanyl)methyl]amino]-3,5,6-tris(oxidanyl)cyclohexyl]oxy-4-[bis(oxidanyl)methyl]-5-methyl-4-oxidanyl-oxolan-3-yl]oxy-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-3-yl]-methyl-azanium / hydrated form of streptomycin


Mass: 602.613 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H44N7O13 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.71 Å3/Da / Density % sol: 54.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium malate, 10 % PEG 3350, 10 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.979493 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jul 9, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979493 Å / Relative weight: 1
ReflectionResolution: 1.85→127.57 Å / Num. obs: 34637 / % possible obs: 100 % / Redundancy: 20.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.339 / Rpim(I) all: 0.076 / Rrim(I) all: 0.347 / Net I/σ(I): 10.6 / Num. measured all: 708684
Reflection shellResolution: 1.85→1.95 Å / % possible obs: 100 % / Redundancy: 21.1 % / Rmerge(I) obs: 4.272 / Num. measured all: 104983 / Num. unique obs: 4977 / CC1/2: 0.513 / Rpim(I) all: 0.945 / Rrim(I) all: 4.376 / Net I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALAdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→45 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 1712 4.96 %
Rwork0.1717 --
obs0.1731 34514 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2368 0 46 320 2734
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.074
X-RAY DIFFRACTIONf_dihedral_angle_d10.837396
X-RAY DIFFRACTIONf_chiral_restr0.068380
X-RAY DIFFRACTIONf_plane_restr0.008422
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.90.31681280.27682690X-RAY DIFFRACTION99
1.9-1.970.28761300.23372704X-RAY DIFFRACTION100
1.97-2.040.28451420.20762706X-RAY DIFFRACTION100
2.04-2.120.21831220.18372684X-RAY DIFFRACTION100
2.12-2.210.18931410.18692711X-RAY DIFFRACTION100
2.21-2.330.1951520.17362692X-RAY DIFFRACTION100
2.33-2.480.2111240.18182731X-RAY DIFFRACTION100
2.48-2.670.19031610.17652717X-RAY DIFFRACTION100
2.67-2.940.21021340.18712764X-RAY DIFFRACTION100
2.94-3.360.19631550.16922732X-RAY DIFFRACTION100
3.36-4.230.17661780.14762752X-RAY DIFFRACTION100
4.23-450.17431450.14772919X-RAY DIFFRACTION100

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