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- PDB-2ard: The structure of tryptophan 7-halogenase (PrnA) suggests a mechan... -

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Basic information

Entry
Database: PDB / ID: 2ard
TitleThe structure of tryptophan 7-halogenase (PrnA) suggests a mechanism for regioselective chlorination
Componentstryptophan halogenase PrnA
KeywordsBIOSYNTHETIC PROTEIN / tryptophan 7-halogenase / flavin-dependent halogenase / helical bundle / sandwiched sheets / Structural Genomics / Scottish Structural Proteomics Facility / SSPF
Function / homology
Function and homology information


tryptophan 7-halogenase / antibiotic biosynthetic process / monooxygenase activity / nucleotide binding
Similarity search - Function
Flavin-dependent tryptophan halogenase / Flavin-dependent halogenase / Tryptophan halogenase / : / 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
DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Tryptophan 7-halogenase PrnA
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDong, C. / Flecks, S. / Unversucht, S. / Haupt, C. / Van Pee, K.H. / Naismith, J.H. / Scottish Structural Proteomics Facility (SSPF)
Citation
Journal: Science / Year: 2005
Title: Tryptophan 7-halogenase (PrnA) structure suggests a mechanism for regioselective chlorination.
Authors: Dong, C. / Flecks, S. / Unversucht, S. / Haupt, C. / van Pee, K.H. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and X-ray diffraction of a halogenating enzyme, tryptophan 7-halogenase, from Pseudomonas fluorescens
Authors: Dong, C. / Kotzsch, A. / Dorward, M. / Van Pee, K.H. / Naismith, J.H.
History
DepositionAug 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Dec 9, 2015Group: Derived calculations
Revision 1.4Aug 23, 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

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Assembly

Deposited unit
A: tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9342
Polymers61,1461
Non-polymers7881
Water1,67593
1
A: tryptophan halogenase PrnA
hetero molecules

A: tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,8674
Polymers122,2922
Non-polymers1,5752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+3/2,y+1/2,-z+3/41
Unit cell
Length a, b, c (Å)68.300, 68.300, 274.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein tryptophan halogenase PrnA


Mass: 61146.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: prnA / Plasmid: pPEH14 / Production host: Pseudomonas fluorescens (bacteria) / Strain (production host): Pseudomonas fluorescens BL915 / References: UniProt: P95480
#2: Chemical ChemComp-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.6 Å3/Da / Density % sol: 52.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% PEG20000, 0.1M Mes pH6.5, 5mM FAD, 30mM sodium dithionite , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→54.82 Å / % possible obs: 98.2 % / Observed criterion σ(F): 11.5 / Observed criterion σ(I): 2.5 / Redundancy: 3.97 % / Biso Wilson estimate: 57.69 Å2 / Rmerge(I) obs: 0.092 / Rsym value: 0.089 / Χ2: 0.81 / Net I/σ(I): 8 / Scaling rejects: 628
Reflection shellResolution: 2.59→2.69 Å / % possible obs: 96.3 % / Redundancy: 3.87 % / Rmerge(I) obs: 0.321 / Mean I/σ(I) obs: 3.3 / Num. measured obs: 126 / Num. unique all: 1872 / Rsym value: 0.32 / Χ2: 0.9 / % possible all: 96.3

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
d*TREKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AR8

2ar8


Resolution: 2.6→54.8 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.898 / SU B: 25.619 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.648 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1068 5.1 %RANDOM
Rwork0.211 ---
all0.214 ---
obs0.21 20795 98.52 %-
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: 29.698 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2--0.25 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2.6→54.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4008 0 53 93 4154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224175
X-RAY DIFFRACTIONr_angle_refined_deg1.81.9585678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8215500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55323.235204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59415653
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2541533
X-RAY DIFFRACTIONr_chiral_restr0.1130.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023254
X-RAY DIFFRACTIONr_nbd_refined0.2390.21952
X-RAY DIFFRACTIONr_nbtor_refined0.3240.22805
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2188
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.213
X-RAY DIFFRACTIONr_mcbond_it0.7211.52557
X-RAY DIFFRACTIONr_mcangle_it1.29324026
X-RAY DIFFRACTIONr_scbond_it1.98631870
X-RAY DIFFRACTIONr_scangle_it3.2324.51652
LS refinement shellResolution: 2.598→2.665 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 73 -
Rwork0.258 1435 -
all-1508 -
obs-7746 99.6 %
Refinement TLS params.Method: refined / Origin x: 41.336 Å / Origin y: 23.754 Å / Origin z: 89.306 Å
111213212223313233
T0.3635 Å20.0338 Å2-0.0708 Å2-0.1025 Å2-0.0049 Å2--0.1549 Å2
L0.5691 °20.6616 °20.2221 °2-1.791 °20.0932 °2--0.8646 °2
S0.2078 Å °0.0483 Å °-0.0188 Å °0.3484 Å °0.0203 Å °0.0329 Å °0.1132 Å °-0.0249 Å °-0.2281 Å °
Refinement TLS groupSelection: ALL

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