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- PDB-2ar8: The structure of tryptophan 7-halogenase (PrnA)suggests a mechani... -

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Basic information

Entry
Database: PDB / ID: 2ar8
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
7-CHLOROTRYPTOPHAN / FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 7-halogenase PrnA
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 1.3Aug 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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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)62,2064
Polymers61,1461
Non-polymers1,0603
Water4,071226
1
A: tryptophan halogenase PrnA
hetero molecules

A: tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4128
Polymers122,2922
Non-polymers2,1196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x+1/2,-y+1/2,-z+1/41
Unit cell
Length a, b, c (Å)67.128, 67.128, 275.702
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CTE / 7-CHLOROTRYPTOPHAN


Type: L-peptide linking / Mass: 238.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11ClN2O2
#4: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 8% PEG20000, 0.1M Mes pH6.5, 20mM 7-chlorotryptophan, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.2→54.4 Å / Num. obs: 33547 / % possible obs: 99.7 % / Observed criterion σ(F): 3.1 / Observed criterion σ(I): 1.8 / Redundancy: 14.1 % / Biso Wilson estimate: 29.25 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 4.5
Reflection shellResolution: 2.2→2.32 Å / % possible obs: 98.7 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 4744 / Num. unique all: 4744 / Rsym value: 0.375 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AQJ

2aqj


Resolution: 2.2→54.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 9.518 / SU ML: 0.127 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1671 5 %RANDOM
Rwork0.172 ---
all0.174 ---
obs0.173 33129 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: 25.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20 Å20 Å2
2--0.33 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.2→54.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 70 226 4458
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224353
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.9615921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.275516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.05223.194216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13615687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8851535
X-RAY DIFFRACTIONr_chiral_restr0.0950.2618
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023395
X-RAY DIFFRACTIONr_nbd_refined0.2110.22174
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23010
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2347
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.210
X-RAY DIFFRACTIONr_mcbond_it0.8361.52646
X-RAY DIFFRACTIONr_mcangle_it1.35824162
X-RAY DIFFRACTIONr_scbond_it2.07332060
X-RAY DIFFRACTIONr_scangle_it3.2724.51759
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 120 -
Rwork0.187 2245 -
all-2365 -
obs-4744 98.17 %
Refinement TLS params.Method: refined / Origin x: 9.882 Å / Origin y: 6.675 Å / Origin z: 20.117 Å
111213212223313233
T-0.0853 Å2-0.0212 Å2-0.0022 Å2-0.0828 Å2-0.0519 Å2---0.0715 Å2
L2.4736 °2-0.7157 °2-0.2422 °2-0.497 °20.1685 °2--0.6732 °2
S0.0445 Å °-0.3623 Å °-0.0703 Å °-0.0118 Å °0.0946 Å °-0.0231 Å °0.0196 Å °0.1192 Å °-0.139 Å °
Refinement TLS groupSelection: ALL

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