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- PDB-5dbj: Crystal structure of halogenase PltA -

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Basic information

Entry
Database: PDB / ID: 5dbj
TitleCrystal structure of halogenase PltA
ComponentsFADH2-dependent halogenase PltA
KeywordsFLAVOPROTEIN / halogenase / FAD / Rossmann fold / pyoluteorin
Function / homology
Function and homology information


1H-pyrrole-2-carbonyl-[peptidyl-carrier protein] chlorinase / alkylhalidase activity / antibiotic biosynthetic process / FAD binding / oxidoreductase activity
Similarity search - Function
Tryptophan halogenase / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 1H-pyrrole-2-carbonyl-[peptidyl-carrier protein] chlorinase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsPang, A.H. / Tsodikov, O.V.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Crystal structure of halogenase PltA from the pyoluteorin biosynthetic pathway.
Authors: Pang, A.H. / Garneau-Tsodikova, S. / Tsodikov, O.V.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: FADH2-dependent halogenase PltA
A: FADH2-dependent halogenase PltA
B: FADH2-dependent halogenase PltA
C: FADH2-dependent halogenase PltA
D: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,20219
Polymers256,9555
Non-polymers4,24714
Water1,982110
1
E: FADH2-dependent halogenase PltA
hetero molecules

E: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4958
Polymers102,7822
Non-polymers1,7136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1880 Å2
ΔGint-7 kcal/mol
Surface area33320 Å2
MethodPISA
2
A: FADH2-dependent halogenase PltA
B: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4958
Polymers102,7822
Non-polymers1,7136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-7 kcal/mol
Surface area33420 Å2
MethodPISA
3
C: FADH2-dependent halogenase PltA
D: FADH2-dependent halogenase PltA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4607
Polymers102,7822
Non-polymers1,6775
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-9 kcal/mol
Surface area33480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)242.934, 94.981, 102.145
Angle α, β, γ (deg.)90.00, 91.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
FADH2-dependent halogenase PltA


Mass: 51391.062 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (strain Pf-5 / ATCC BAA-477) (bacteria)
Strain: Pf-5 / ATCC BAA-477 / Gene: pltA, PFL_2787 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q4KCZ0, alkylhalidase
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / 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: 46.35 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M Bis-Tris propane, pH 7.0, 50 mM magnesium sulfate heptahydrate, 20% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX300HS / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 56814 / % possible obs: 95.1 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.6
Reflection shellResolution: 2.7→2.8 Å / Rmerge(I) obs: 0.59

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Processing

Software
NameVersionClassification
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NIX

3nix


Resolution: 2.75→40 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.887 / SU B: 51.317 / SU ML: 0.447 / Cross valid method: THROUGHOUT / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29165 2916 5.1 %RANDOM
Rwork0.23886 ---
obs0.24147 54814 95.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.222 Å2
Baniso -1Baniso -2Baniso -3
1-3.9 Å20 Å21.24 Å2
2--1.28 Å20 Å2
3----5.23 Å2
Refinement stepCycle: LAST / Resolution: 2.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17370 0 274 110 17754
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01918062
X-RAY DIFFRACTIONr_bond_other_d0.0060.0216915
X-RAY DIFFRACTIONr_angle_refined_deg1.231.96224463
X-RAY DIFFRACTIONr_angle_other_deg0.882338903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83252169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04724.048872
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.779153043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.20315107
X-RAY DIFFRACTIONr_chiral_restr0.0670.22628
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0220333
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024297
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.634.5358699
X-RAY DIFFRACTIONr_mcbond_other0.634.5358698
X-RAY DIFFRACTIONr_mcangle_it1.1596.80210861
X-RAY DIFFRACTIONr_mcangle_other1.1596.80210862
X-RAY DIFFRACTIONr_scbond_it0.3954.5679362
X-RAY DIFFRACTIONr_scbond_other0.3954.5679363
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7726.82613602
X-RAY DIFFRACTIONr_long_range_B_refined3.16936.17720826
X-RAY DIFFRACTIONr_long_range_B_other3.16736.16720820
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 245 -
Rwork0.313 3976 -
obs--95.33 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.44330.28430.11441.2010.9793.16130.1490.06970.30580.14360.1094-0.23310.15150.1158-0.25850.2764-0.0137-0.07660.02040.03260.386436.4546-37.37195.1423
21.98570.0450.9941.3215-0.56963.0763-0.4628-0.79820.4744-0.00540.2003-0.1337-0.6459-1.39740.26250.36850.3205-0.16360.7753-0.25860.21455.2148-26.0778-24.7667
31.41150.4475-0.21141.3287-0.08931.24950.0117-0.1853-0.22310.09470.00330.06870.0776-0.0524-0.0150.3970.0392-0.14950.06390.04870.194581.8006-41.402531.1515
43.2394-0.17240.61061.10560.30330.9482-0.08090.410.0319-0.38050.10770.1049-0.09270.1612-0.02680.5957-0.0703-0.10510.07160.0030.162882.001-36.3491-12.6601
51.98190.54220.04491.33940.01171.3047-0.11780.089-0.31460.02230.0571-0.15120.04850.28910.06070.30170.0473-0.00990.0767-0.01450.217421.0712-57.238847.8346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 438
2X-RAY DIFFRACTION2B2 - 438
3X-RAY DIFFRACTION3C2 - 438
4X-RAY DIFFRACTION4D2 - 438
5X-RAY DIFFRACTION5E2 - 438

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