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- PDB-3jum: Crystal Structure of PhzA/B from Burkholderia cepacia R18194 in c... -

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Basic information

Entry
Database: PDB / ID: 3jum
TitleCrystal Structure of PhzA/B from Burkholderia cepacia R18194 in complex with 5-bromo-2-((1S,3R)-3-carboxycyclohexylamino)benzoic acid
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / chirality / drug design / phenazine biosynthesis / medicinal chemistry / inhibitor
Function / homology
Function and homology information


antibiotic biosynthetic process
Similarity search - Function
Phenazine biosynthesis protein A/B / Phenazine biosynthesis protein A/B / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-AOD / Phenazine biosynthesis protein A/B
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.45 Å
AuthorsMentel, M. / Breinbauer, R. / Blankenfeldt, W.
Citation
Journal: Angew.Chem.Int.Ed.Engl. / Year: 2009
Title: The Active Site of an Enzyme Can Host Both Enantiomers of a Racemic Ligand Simultaneously
Authors: Mentel, M. / Blankenfeldt, W. / Breinbauer, R.
#1: Journal: J.Am.Chem.Soc. / Year: 2008
Title: PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis
Authors: Ahuja, E.G. / Janning, P. / Graebsch, A. / Breinbauer, R. / Hiller, W. / Costisella, B. / Thomashow, L.S. / Mavrodi, D.V. / Blankenfeldt, W.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Phenazine biosynthesis protein A/B
B: Phenazine biosynthesis protein A/B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7464
Polymers43,0622
Non-polymers6842
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4330 Å2
ΔGint-17 kcal/mol
Surface area14740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.690, 64.690, 160.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Phenazine biosynthesis protein A/B


Mass: 21531.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia sp. (bacteria) / Strain: 383 / Gene: Bcep18194_B1568 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) pLysS / References: UniProt: Q396C9
#2: Chemical ChemComp-AOD / 5-bromo-2-{[(1S,3R)-3-carboxycyclohexyl]amino}benzoic acid


Mass: 342.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H16BrNO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 284 K
Details: 16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 5 mM 5-bromo-2-((1S,3R)-3-carboxycyclohexylamino)benzoic ...Details: 16-20% (w/v) PEG3350, 0.2 M NH4OAc, 0.1 M Bis-Tris pH 6.1-6.7; complex prepared by overnight soaking in mother liquor containing 5 mM 5-bromo-2-((1S,3R)-3-carboxycyclohexylamino)benzoic acid, vapor diffusion, hanging drop, temperature 284K
PH range: 6.1 - 6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98407
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 27, 2007 / Details: SI(111)
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98407 Å / Relative weight: 1
ReflectionResolution: 1.45→19.69 Å / Num. obs: 69627 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.15 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.94
Reflection shellResolution: 1.45→1.55 Å / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 3.7 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
RefinementResolution: 1.45→19.69 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.003 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 3557 5.1 %RANDOM
Rwork0.138 ---
obs0.14 69623 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.92 Å2
Refinement stepCycle: LAST / Resolution: 1.45→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 40 379 3038
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0212817
X-RAY DIFFRACTIONr_bond_other_d0.0020.022010
X-RAY DIFFRACTIONr_angle_refined_deg2.1121.9253827
X-RAY DIFFRACTIONr_angle_other_deg1.0793.0024763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.99522.917168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86715458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6151534
X-RAY DIFFRACTIONr_chiral_restr0.510.2369
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023234
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02659
X-RAY DIFFRACTIONr_nbd_refined0.2660.2581
X-RAY DIFFRACTIONr_nbd_other0.230.22240
X-RAY DIFFRACTIONr_nbtor_refined0.1950.21350
X-RAY DIFFRACTIONr_nbtor_other0.0930.21607
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.2283
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3870.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.390.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0461.52036
X-RAY DIFFRACTIONr_mcbond_other1.1051.5653
X-RAY DIFFRACTIONr_mcangle_it3.48722591
X-RAY DIFFRACTIONr_scbond_it5.03831429
X-RAY DIFFRACTIONr_scangle_it6.7534.51229
X-RAY DIFFRACTIONr_rigid_bond_restr2.67736140
X-RAY DIFFRACTIONr_sphericity_free14.0423379
X-RAY DIFFRACTIONr_sphericity_bonded4.90934738
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 263 -
Rwork0.153 4781 -
obs--99.41 %
Refinement TLS params.Method: refined / Origin x: 36.6551 Å / Origin y: 5.898 Å / Origin z: 79.367 Å
111213212223313233
T-0.0426 Å20.0068 Å2-0.0007 Å2--0.0244 Å2-0.0038 Å2---0.0357 Å2
L0.4855 °2-0.0421 °20.1847 °2-0.6484 °2-0.2801 °2--0.8169 °2
S0.0007 Å °0.0133 Å °0.0156 Å °-0.0357 Å °0.0286 Å °-0.0324 Å °0.0286 Å °-0.0283 Å °-0.0293 Å °

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