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- PDB-8agy: The Corramycin phosphotransferase in complex with Corramycin -

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Basic information

Entry
Database: PDB / ID: 8agy
TitleThe Corramycin phosphotransferase in complex with Corramycin
Components
  • Corramycin
  • Corramycin phosphotransferase
KeywordsTRANSFERASE / Phosphotransferase / Complex / Resistance protein
Function / homologyAminoglycoside 3'-phosphotransferase; Chain: A, domain 2 / Aminoglycoside phosphotransferase (APH), C-terminal lobe / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesCorallococcus coralloides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsAdam, S. / Mueller, R. / Koehnke, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: To Be Published
Title: The Corramycin phosphotransferase in complex with Corramycin
Authors: Adam, S. / Mueller, R. / Koehnke, J.
History
DepositionJul 20, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_validate_peptide_omega.auth_comp_id_1 / _pdbx_validate_peptide_omega.auth_comp_id_2 / _pdbx_validate_peptide_omega.auth_seq_id_1 / _pdbx_validate_peptide_omega.auth_seq_id_2 / _pdbx_validate_peptide_omega.omega
Revision 2.1Apr 23, 2025Group: Structure summary
Category: entity / pdbx_entry_details / pdbx_modification_feature
Item: _entity.pdbx_description / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Corramycin phosphotransferase
B: Corramycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3854
Polymers42,2012
Non-polymers1842
Water7,242402
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint1 kcal/mol
Surface area16380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.964, 67.116, 75.553
Angle α, β, γ (deg.)90.000, 93.330, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Corramycin phosphotransferase


Mass: 41017.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ST201330 (DSM24989) / Source: (gene. exp.) Corallococcus coralloides (bacteria) / Production host: Escherichia coli (E. coli)
#2: Protein/peptide Corramycin


Type: Peptide-like / Class: Antibiotic, Antimicrobial / Mass: 1184.253 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Corallococcus coralloides (bacteria) / References: BIRD: PRD_002426
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / Source method: isolated from a natural source / Formula: H2O
Compound detailspeptide antibiotic with bioactivity against Gram-negative bacteri
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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: PEG 10000, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.5→42.89 Å / Num. obs: 67775 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 16.95 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 22.7
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.442 / Num. unique obs: 9808

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Cootmodel building
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Apo structure

Resolution: 1.5→42.89 Å / SU ML: 0.1552 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0597
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1937 3392 5.01 %
Rwork0.1746 64318 -
obs0.1755 67710 98.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.81 Å2
Refinement stepCycle: LAST / Resolution: 1.5→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 95 402 3259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642947
X-RAY DIFFRACTIONf_angle_d1.00354001
X-RAY DIFFRACTIONf_chiral_restr0.0573420
X-RAY DIFFRACTIONf_plane_restr0.0127522
X-RAY DIFFRACTIONf_dihedral_angle_d6.1554412
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.22741290.21142595X-RAY DIFFRACTION96.02
1.52-1.540.23321550.19662700X-RAY DIFFRACTION99.2
1.54-1.570.22811360.19082656X-RAY DIFFRACTION99.39
1.57-1.590.27421480.222721X-RAY DIFFRACTION99.03
1.59-1.620.25871420.20812633X-RAY DIFFRACTION99
1.62-1.650.24291290.1952708X-RAY DIFFRACTION99.09
1.65-1.680.21311330.18352667X-RAY DIFFRACTION98.87
1.68-1.720.20431470.17962696X-RAY DIFFRACTION98.82
1.72-1.750.20921400.17572622X-RAY DIFFRACTION98.47
1.75-1.80.23061460.17252669X-RAY DIFFRACTION98.29
1.8-1.840.20471290.17582666X-RAY DIFFRACTION98.04
1.84-1.890.19841470.17792634X-RAY DIFFRACTION97.37
1.89-1.950.19221460.18352712X-RAY DIFFRACTION99.83
1.95-2.010.20751450.1872668X-RAY DIFFRACTION99.75
2.01-2.080.18941460.17032696X-RAY DIFFRACTION99.58
2.08-2.160.18441400.17082738X-RAY DIFFRACTION99.41
2.16-2.260.1961210.16962703X-RAY DIFFRACTION99.16
2.26-2.380.1981360.16942672X-RAY DIFFRACTION98.77
2.38-2.530.18291320.17242684X-RAY DIFFRACTION97.88
2.53-2.730.18681590.17562595X-RAY DIFFRACTION96.36
2.73-30.19921420.17392709X-RAY DIFFRACTION99.62
3-3.430.20141520.17442719X-RAY DIFFRACTION99.72
3.43-4.320.15211650.15912715X-RAY DIFFRACTION99.17
4.33-42.890.1981270.17352740X-RAY DIFFRACTION97.38
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.50849027267-0.8292218326090.09589315902293.31194083665-1.059375848980.9838738322530.03093446374270.1092668635290.107776327654-0.08438595263080.1052166219940.4151215805860.0454230027422-0.238303990017-0.1216672393340.134480269176-0.0185243638374-0.009958385604070.1851565819920.04461137034850.14279775351-7.698767058219.29469991038-32.9584035844
20.8522452382290.152839944501-0.2699453054390.993402859259-0.4858801033811.135754218760.00496050150281-0.0212001710691-0.006256397738610.122033420348-0.0172126298272-0.0175687068002-0.0464012714580.06761610364630.01279123898640.1534565626990.00847919768136-0.01003405376940.104206793977-0.001982223801780.1092899131726.98634628281-2.12549899515-16.9288039231
31.522226037160.703256778549-0.6103432726981.49755224047-0.9152319998611.68875181724-0.00968797822794-0.00955812379019-0.1682508438320.02791266108240.03902780135220.007631478585860.142394695907-0.0456398165082-0.04037326051850.1878364651370.03047107773660.005106511652680.1134156910340.01427333610730.132703120324-0.970448800916-14.9060903752-10.6509456288
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 113 )13 - 1131 - 95
22chain 'A' and (resid 114 through 267 )114 - 26796 - 249
33chain 'A' and (resid 268 through 364 )268 - 364250 - 346

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