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- PDB-4z43: Crystal structure of Tryptophan 7-halogenase (PrnA) Mutant E450K -

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Basic information

Entry
Database: PDB / ID: 4z43
TitleCrystal structure of Tryptophan 7-halogenase (PrnA) Mutant E450K
ComponentsFlavin-dependent tryptophan halogenase PrnA
KeywordsOXIDOREDUCTASE / 7-halogenase (PrnA) Mutant E450K
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 / MOLECULAR REPLACEMENT / Resolution: 2.29 Å
AuthorsLevy, C.W.
CitationJournal: Chem Sci / Year: 2015
Title: Extending the biocatalytic scope of regiocomplementary flavin-dependent halogenase enzymes.
Authors: Shepherd, S.A. / Karthikeyan, C. / Latham, J. / Struck, A.W. / Thompson, M.L. / Menon, B.R.K. / Styles, M.Q. / Levy, C. / Leys, D. / Micklefield, J.
History
DepositionApr 1, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)62,0634
Polymers61,1461
Non-polymers9173
Water81145
1
A: Flavin-dependent tryptophan halogenase PrnA
hetero molecules

A: Flavin-dependent tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,1268
Polymers122,2922
Non-polymers1,8346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area7070 Å2
ΔGint-82 kcal/mol
Surface area37960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.740, 68.740, 276.170
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


Mass: 61146.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: prnA / Production host: Escherichia coli (E. coli) / References: UniProt: P95480, tryptophan 7-halogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 1.0 M Imidazole and MES Buffer Mix at pH 6.5, containing 0.09 M nitrate phosphate sulfate salt mix (NaNO3; Na2HPO4; (NH4)2SO4)) and 60% w/v glycerol and polyethylene glycol 4K)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9779 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9779 Å / Relative weight: 1
ReflectionResolution: 2.29→30.85 Å / Num. obs: 30949 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 22.16
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.44 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIXDEV_1977refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AQJ

2aqj


Resolution: 2.29→30.85 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.228 2000 6.46 %
Rwork0.184 --
obs0.187 30949 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→30.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4061 0 59 45 4165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054242
X-RAY DIFFRACTIONf_angle_d0.9095766
X-RAY DIFFRACTIONf_dihedral_angle_d13.6531544
X-RAY DIFFRACTIONf_chiral_restr0.04603
X-RAY DIFFRACTIONf_plane_restr0.004742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.34730.29341380.25031989X-RAY DIFFRACTION100
2.3473-2.41070.31631390.23982023X-RAY DIFFRACTION100
2.4107-2.48160.34511410.23242034X-RAY DIFFRACTION100
2.4816-2.56170.28711410.22622037X-RAY DIFFRACTION100
2.5617-2.65320.29681390.232026X-RAY DIFFRACTION100
2.6532-2.75930.26141410.21682027X-RAY DIFFRACTION100
2.7593-2.88480.28071400.22132034X-RAY DIFFRACTION100
2.8848-3.03680.26481410.22872050X-RAY DIFFRACTION100
3.0368-3.22690.28121420.22032054X-RAY DIFFRACTION100
3.2269-3.47570.25741450.21062077X-RAY DIFFRACTION100
3.4757-3.82490.25141430.17922082X-RAY DIFFRACTION100
3.8249-4.37710.1671440.15162091X-RAY DIFFRACTION100
4.3771-5.50950.17391480.14362140X-RAY DIFFRACTION100
5.5095-30.85230.19181580.15782285X-RAY DIFFRACTION100
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)
11.5209-1.65660.20323.29130.14671.09490.1225-0.0471-0.2319-0.44480.11740.50560.0287-0.1657-0.21440.536-0.05180.03150.2510.04720.4044-30.5688-29.758-19.5619
21.4424-0.8892-0.1932.20620.00971.42110.2424-0.02680.0862-0.74370.05310.0581-0.3284-0.1381-0.19480.74650.02360.12080.24340.03470.4137-29.4304-14.9492-23.7109
31.6622-1.41430.10392.9612-0.26581.51720.1272-0.2977-0.0735-0.09080.17380.05530.12040.0818-0.25240.4983-0.02070.0680.2581-0.05870.3768-18.2016-36.4388-14.4572
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 2 THROUGH 152 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 153 THROUGH 395 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 396 THROUGH 517 )

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