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

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Basic information

Entry
Database: PDB / ID: 2apg
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
FLAVIN-ADENINE DINUCLEOTIDE / Tryptophan 7-halogenase PrnA
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 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 16, 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 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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)62,0634
Polymers61,1461
Non-polymers9173
Water7,278404
1
A: tryptophan halogenase PrnA
hetero molecules

A: tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1268
Polymers122,2922
Non-polymers1,8346
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)67.520, 67.520, 275.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-1069-

HOH

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#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.: 404 / 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 growMethod: vapor diffusion, sitting drop / pH: 8
Details: 10% PEG8000, 0.1M imidazole pH8.0, 0.2M Ca(CH3CO2)2, VAPOR DIFFUSION, SITTING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2003 / Details: mirrors
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→69.01 Å / Num. all: 66245 / Num. obs: 48481 / % possible obs: 98 % / Observed criterion σ(F): 7.8 / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 23.988 Å2 / Rmerge(I) obs: 0.132 / Rsym value: 0.113 / Net I/σ(I): 3.8
Reflection shellResolution: 1.9→1.949 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 1 / Num. unique all: 3759 / Rsym value: 0.484 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0007refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→69.01 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.568 / SU ML: 0.087 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 7.8 / σ(I): 3 / ESU R: 0.134 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 2610 5.1 %RANDOM
Rwork0.17631 ---
all0.1781 51779 --
obs0.175 48481 99.2 %-
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: 24.407 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.02 Å0.021 Å
Luzzati d res low-4 Å
Luzzati sigma a0.3 Å0.082 Å
Refinement stepCycle: LAST / Resolution: 1.9→69.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 59 404 4625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224340
X-RAY DIFFRACTIONr_angle_refined_deg1.5441.9585903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28123.194216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.4315687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9041535
X-RAY DIFFRACTIONr_chiral_restr0.10.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023380
X-RAY DIFFRACTIONr_nbd_refined0.2140.22220
X-RAY DIFFRACTIONr_nbtor_refined0.3160.23020
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2436
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1690.279
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.228
X-RAY DIFFRACTIONr_mcbond_it0.9591.52645
X-RAY DIFFRACTIONr_mcangle_it1.43424155
X-RAY DIFFRACTIONr_scbond_it2.33632039
X-RAY DIFFRACTIONr_scangle_it3.5184.51748
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 207 -
Rwork0.211 3494 -
obs-3494 99.28 %
Refinement TLS params.Method: refined / Origin x: 9.801 Å / Origin y: 6.531 Å / Origin z: 20.212 Å
111213212223313233
T-0.0785 Å2-0.0144 Å2-0.0001 Å2-0.0541 Å2-0.0528 Å2---0.02 Å2
L1.3223 °2-0.4121 °2-0.0953 °2-0.3857 °20.046 °2--0.7131 °2
S0.0346 Å °-0.226 Å °-0.0293 Å °0.0107 Å °0.0704 Å °-0.0235 Å °0.0014 Å °0.0897 Å °-0.105 Å °

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