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- PDB-4k7t: Structure of the ternary complex of bacitracin, zinc, and geranyl... -

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Basic information

Entry
Database: PDB / ID: 4k7t
TitleStructure of the ternary complex of bacitracin, zinc, and geranyl-pyrophosphate
Componentsbacitracin A2
KeywordsANTIBIOTIC / bacitracin / cell-wall biosynthesis inhibitor / undecaprenyl-pyrophosphate
Function / homologyBacitracin A1 / GERANYL DIPHOSPHATE / :
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsEconomou, N.J. / Loll, P.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: High-resolution crystal structure reveals molecular details of target recognition by bacitracin.
Authors: Economou, N.J. / Cocklin, S. / Loll, P.J.
History
DepositionApr 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Database references
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Oct 16, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: bacitracin A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,8634
Polymers1,4611
Non-polymers4033
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.980, 35.980, 16.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein/peptide bacitracin A2


Type: Cyclic peptide / Class: Antibiotic / Mass: 1460.740 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus subtilis (bacteria) / References: NOR: NOR00018, Bacitracin A1
#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O
Compound detailsILE-1 AND CYS-2 HAVE UNDERGONE A CONDENSATION REACTION TO PRODUCE A THIAZOLINE RING
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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 6.5
Details: 20% PEG-2000 in 0.1 M sodium acetate pH 6.5, microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Details: Si(111)
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionNumber: 115240 / Rmerge(I) obs: 0.086 / D res high: 1.29 Å / Num. obs: 5949 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
1.291.3244095.910.642
1.321.3643099.810.511
1.361.3939510010.367
1.391.4442510010.315
1.441.4838910010.223
1.481.5436110010.183
1.541.5939110010.147
1.591.6633210010.122
1.661.7335310010.093
1.731.8231710010.089
1.821.9230310010.086
1.922.0330010010.069
2.032.1727710010.07
2.172.3525810010.066
2.352.5723610010.067
2.572.8720599.510.062
2.873.3219210010.059
3.324.0716110010.055
4.075.7512110010.062
ReflectionResolution: 1.1→12.005 Å / Num. obs: 4983 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.6 % / Biso Wilson estimate: 11.547 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 16.69
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.1-1.160.6694.1144461423199.9
1.16-1.240.4156.451531114621100
1.24-1.340.24110.21453213711100
1.34-1.470.15914.471367212751100
1.47-1.640.10919.711190311041100
1.64-1.890.07725.02106549901100
1.89-2.310.06232.0790628531100
2.31-3.240.05635.076783647199.8
3.24-200.06138.783738363199.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→12.005 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8966 / SU ML: 0.08 / σ(F): 1.22 / Phase error: 17.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1493 438 4.62 %random
Rwork0.1271 ---
obs0.1284 4983 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 30.95 Å2 / Biso mean: 12.6637 Å2 / Biso min: 5.78 Å2
Refinement stepCycle: LAST / Resolution: 1.1→12.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms100 0 21 20 141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008121
X-RAY DIFFRACTIONf_angle_d2.051164
X-RAY DIFFRACTIONf_chiral_restr0.1216
X-RAY DIFFRACTIONf_plane_restr0.00519
X-RAY DIFFRACTIONf_dihedral_angle_d15.38139
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 3 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.1-1.2590.16331160.137630443160
1.259-1.58560.13391710.112829913162
1.5856-12.00610.15451510.130430073158

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