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- PDB-3b4o: Crystal structure of phenazine biosynthesis protein PhzA/B from B... -

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Basic information

Entry
Database: PDB / ID: 3b4o
TitleCrystal structure of phenazine biosynthesis protein PhzA/B from Burkholderia cepacia R18194, apo form
ComponentsPhenazine biosynthesis protein A/B
KeywordsBIOSYNTHETIC PROTEIN / phenazine biosynthesis / imine / Schiff base
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
ACETATE ION / Phenazine biosynthesis protein A/B
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsAhuja, E.G. / Janning, P. / Mentel, M. / Graebsch, A. / Breinbauer, R. / Blankenfeldt, W.
CitationJournal: J.Am.Chem.Soc. / Year: 2008
Title: PhzA/B catalyzes the formation of the tricycle in phenazine biosynthesis.
Authors: Ahuja, E.G. / Janning, P. / Mentel, M. / Graebsch, A. / Breinbauer, R. / Hiller, W. / Costisella, B. / Thomashow, L.S. / Mavrodi, D.V. / Blankenfeldt, W.
History
DepositionOct 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)43,2986
Polymers43,0622
Non-polymers2364
Water2,810156
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.660, 64.660, 160.950
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: R18194 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 pLysS / References: UniProt: Q396C9
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 16 20% (w/v) PEG 3350, 0.2 M NH4-acetate, 0.1 M Bis-TRIS pH 6.1 6.7, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 22, 2006 / Details: Si(111)monochromator
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 31581 / Num. obs: 31421 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 8.3 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 19.3
Reflection shellResolution: 1.9→2 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 3.9 / Num. unique all: 4408 / % possible all: 99.4

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
XDSdata scaling
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
RefinementResolution: 1.9→19.69 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.611 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.305 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1582 5 %RANDOM
Rwork0.186 ---
obs0.188 31420 99.62 %-
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: 38.187 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2701 0 16 156 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212799
X-RAY DIFFRACTIONr_bond_other_d0.0010.021984
X-RAY DIFFRACTIONr_angle_refined_deg1.6861.9153795
X-RAY DIFFRACTIONr_angle_other_deg1.04134734
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7095331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69722.874167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02515457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6341534
X-RAY DIFFRACTIONr_chiral_restr0.2230.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023241
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02661
X-RAY DIFFRACTIONr_nbd_refined0.2060.2530
X-RAY DIFFRACTIONr_nbd_other0.2150.22027
X-RAY DIFFRACTIONr_nbtor_refined0.180.21306
X-RAY DIFFRACTIONr_nbtor_other0.0850.21535
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2760.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.28
X-RAY DIFFRACTIONr_mcbond_it2.4671.52104
X-RAY DIFFRACTIONr_mcbond_other3.0651.5658
X-RAY DIFFRACTIONr_mcangle_it3.12122623
X-RAY DIFFRACTIONr_scbond_it4.36831390
X-RAY DIFFRACTIONr_scangle_it6.0144.51172
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 125 -
Rwork0.263 2130 -
all-2255 -
obs--99.38 %

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