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- PDB-3cnm: Crystal Structure of Phenazine Biosynthesis Protein PhzA/B from B... -

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Basic information

Entry
Database: PDB / ID: 3cnm
TitleCrystal Structure of Phenazine Biosynthesis Protein PhzA/B from Burkholderia cepacia R18194, DHHA complex
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 / Chem-HHA / Phenazine biosynthesis protein A/B
Similarity search - Component
Biological speciesBurkholderia sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement of apo structure / Resolution: 1.65 Å
AuthorsAhuja, E.G. / 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
DepositionMar 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)43,5497
Polymers43,0622
Non-polymers4875
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6010 Å2
ΔGint-14.5 kcal/mol
Surface area14950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.090, 65.090, 161.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Detailsdimer

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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): Rosetta pLysS / References: UniProt: Q396C9
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-HHA / (2S,3S)-TRANS-2,3-DIHYDRO-3-HYDROXYANTHRANILIC ACID


Mass: 155.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H9NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.1
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 50 mM DHHA, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9809 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 6, 2008 / Details: SI(111) monochromator
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9809 Å / Relative weight: 1
ReflectionResolution: 1.65→20 Å / Num. all: 48683 / Num. obs: 48675 / % possible obs: 100 % / Observed criterion σ(I): 3 / Redundancy: 14.1 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.139 / Net I/σ(I): 16
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.7 / Num. unique all: 7754 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: rigid body refinement of apo structure
Starting model: 3B4O

3b4o


Resolution: 1.65→19.81 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.958 / SU B: 3.23 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; TLS-Refinement was used throughout (1 TLS body)
RfactorNum. reflection% reflectionSelection details
Rfree0.1939 2447 5 %RANDOM
Rwork0.15469 ---
obs0.15662 46189 99.99 %-
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: 24.467 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2619 0 34 377 3030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.0212841
X-RAY DIFFRACTIONr_bond_other_d0.0020.022018
X-RAY DIFFRACTIONr_angle_refined_deg2.3191.923863
X-RAY DIFFRACTIONr_angle_other_deg1.1033.0014816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0145342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32323.023172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915469
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7581534
X-RAY DIFFRACTIONr_chiral_restr0.1620.2375
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.023268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02662
X-RAY DIFFRACTIONr_nbd_refined0.2410.2522
X-RAY DIFFRACTIONr_nbd_other0.2230.22109
X-RAY DIFFRACTIONr_nbtor_refined0.190.21306
X-RAY DIFFRACTIONr_nbtor_other0.0890.21528
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.2256
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.410.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3420.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3610.214
X-RAY DIFFRACTIONr_mcbond_it2.2051.52117
X-RAY DIFFRACTIONr_mcbond_other0.531.5657
X-RAY DIFFRACTIONr_mcangle_it2.45722623
X-RAY DIFFRACTIONr_scbond_it431428
X-RAY DIFFRACTIONr_scangle_it5.6864.51227
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.245 165 -
Rwork0.171 3361 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 37.0061 Å / Origin y: 5.9718 Å / Origin z: 79.8364 Å
111213212223313233
T-0.0908 Å20.007 Å20.0034 Å2--0.0724 Å2-0.0128 Å2---0.0599 Å2
L0.8688 °2-0.1781 °20.3567 °2-1.3452 °2-0.7116 °2--1.6569 °2
S-0.0139 Å °0.0522 Å °0.0372 Å °-0.0525 Å °0.0437 Å °-0.0875 Å °0.0301 Å °-0.037 Å °-0.0298 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1B601 - 779
2X-RAY DIFFRACTION1A801 - 998
3X-RAY DIFFRACTION1B500 - 600
4X-RAY DIFFRACTION1A500 - 800
5X-RAY DIFFRACTION1B8 - 165
6X-RAY DIFFRACTION1A9 - 165

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