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- PDB-2jkc: Crystal Structure of E346D of Tryptophan 7-Halogenase (PrnA) -

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Basic information

Entry
Database: PDB / ID: 2jkc
TitleCrystal Structure of E346D of Tryptophan 7-Halogenase (PrnA)
ComponentsFlavin-dependent tryptophan halogenase PrnA
KeywordsOXIDOREDUCTASE / ENZYMATIC HALOGENATION / TRYPTOPHAN HALOGENASE / FLAVIN- DEPENDENT REACTION MECHANISM
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 / Tryptophan 7-halogenase PrnA
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, X. / Naismith, J.H.
Citation
Journal: Angew. Chem. Int. Ed. Engl. / Year: 2008
Title: New insights into the mechanism of enzymatic chlorination of tryptophan.
Authors: Flecks, S. / Patallo, E.P. / Zhu, X. / Ernyei, A.J. / Seifert, G. / Schneider, A. / Dong, C. / Naismith, J.H. / van Pee, K.H.
#1: 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. / Vanpee, K. / Naismith, J.
History
DepositionAug 26, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 29, 2012Group: Database references
Revision 1.3Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 3, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: citation / citation_author ...citation / citation_author / entity / entity_src_gen / entity_src_nat / struct_ref
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity.pdbx_description / _entity.pdbx_ec / _entity.src_method / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.5Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details ..._pdbx_database_status.status_code_sf / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.6Dec 13, 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: Flavin-dependent tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1935
Polymers61,1321
Non-polymers1,0614
Water7,134396
1
A: Flavin-dependent tryptophan halogenase PrnA
hetero molecules

A: Flavin-dependent tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,38510
Polymers122,2642
Non-polymers2,1218
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7190 Å2
ΔGint-82 kcal/mol
Surface area38410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.360, 68.360, 276.630
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 Flavin-dependent tryptophan halogenase PrnA / TRYPTOPHAN 7-HALOGENASE


Mass: 61132.062 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: prnA / Production host: Pseudomonas fluorescens (bacteria) / Strain (production host): BL915 / References: UniProt: P95480, tryptophan 7-halogenase
#2: Chemical ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 346 TO ASP
Sequence detailsE346D MUTATION

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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: 53.5 % / Description: NONE
Crystal growpH: 10 / Details: 0.1M CHES PH10 0.2M NACL 1.6 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Aug 22, 2008 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→28.1 Å / Num. obs: 29779 / % possible obs: 96.6 % / Observed criterion σ(I): 2 / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.3
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 5 / % possible all: 85

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALAdata scaling
REFMACRIGID BODY REFINEMENTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AQJ

2aqj


Resolution: 2.3→28.13 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.327 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.265 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21 1527 5.1 %RANDOM
Rwork0.161 ---
obs0.164 28173 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.3→28.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4153 0 70 396 4619
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0224371
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.9555948
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6165521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.05623.119218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89915692
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3611536
X-RAY DIFFRACTIONr_chiral_restr0.090.2620
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023414
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.21878
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22952
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2352
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1980.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6331.52672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.05924185
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.67432042
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.6494.51763
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.292 93
Rwork0.201 1709
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)
10.2322-0.3631-0.10441.2064-0.0120.5625-0.0117-0.0345-0.0157-0.04610.07630.0993-0.036-0.0238-0.0646-0.0007-0.00690.0389-0.0920.0013-0.05326.64869.3632-20.3534
21.5766-0.7573-1.78360.86731.60693.1355-0.326-0.4766-0.2289-0.72440.83790.24430.0774-0.6215-0.51190.014-0.0391-0.00050.01390.0252-0.00882.443720.4637-27.3857
342.3386-24.9452-46.192752.917-4.729677.0987-0.09160.99830.76860.3992-0.40450.3468-0.59730.39720.49610.00570.00280.00490.0012-0.00050.00017.38813.8593-16.2664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 517
2X-RAY DIFFRACTION2A1518
3X-RAY DIFFRACTION2A1521
4X-RAY DIFFRACTION3A1520

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