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- PDB-4nag: Xanthomonins I III are a New Class of Lasso Peptides Featuringa S... -

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Basic information

Entry
Database: PDB / ID: 4nag
TitleXanthomonins I III are a New Class of Lasso Peptides Featuringa Seven-Membered Macrolactam Ring
ComponentsXanthomonin I
KeywordsBIOSYNTHETIC PROTEIN / biosynthesis / lasso peptides / natural products / macrocycles / steric hindrance / Lariat knot / Lasso fold
Function / homologyHEXANE-1,6-DIOL / Uncharacterized protein
Function and homology information
Biological speciesXanthomonas gardneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 0.81 Å
AuthorsHegemann, J.D. / Zimmermann, M. / Zhu, S. / Steuber, H. / Harms, K. / Xie, X. / Marahiel, M.A.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Xanthomonins I-III: A New Class of Lasso Peptides with a Seven-Residue Macrolactam Ring.
Authors: Hegemann, J.D. / Zimmermann, M. / Zhu, S. / Steuber, H. / Harms, K. / Xie, X. / Marahiel, M.A.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xanthomonin I
B: Xanthomonin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,0593
Polymers2,9412
Non-polymers1181
Water66737
1
A: Xanthomonin I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,5892
Polymers1,4711
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Xanthomonin I


Theoretical massNumber of molelcules
Total (without water)1,4711
Polymers1,4711
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)13.804, 45.096, 13.890
Angle α, β, γ (deg.)90.00, 91.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Xanthomonin I


Mass: 1470.584 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas gardneri (bacteria) / Strain: ATCC 19865 / Gene: XGA_4058 / Production host: Escherichia coli (E. coli) / References: UniProt: F0CAT0
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.47 Å3/Da / Density % sol: 16.3 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.8 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.81→23.55 Å / Num. all: 24760 / Num. obs: 23992 / % possible obs: 84.6 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 0.81→23.55 Å / Num. parameters: 2161 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: AUTHOR CONFIRMED THAT R-FREE WAS NOT USED.
RfactorNum. reflection% reflection
all0.054 24760 -
obs-23992 85 %
Refine analyzeNum. disordered residues: 2 / Occupancy sum hydrogen: 210 / Occupancy sum non hydrogen: 232.8
Refinement stepCycle: LAST / Resolution: 0.81→23.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms206 0 8 37 251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0284
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.04
X-RAY DIFFRACTIONs_similar_adp_cmpnt0
X-RAY DIFFRACTIONs_approx_iso_adps0

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