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- PDB-4z44: F454K Mutant of Tryptophan 7-halogenase PrnA -

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Basic information

Entry
Database: PDB / ID: 4z44
TitleF454K Mutant of Tryptophan 7-halogenase PrnA
ComponentsFlavin-dependent tryptophan halogenase PrnA
KeywordsOXIDOREDUCTASE
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 / PHOSPHATE ION / Tryptophan 7-halogenase PrnA
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsShepherd, S.A. / Karthikeyan, C. / Latham, J. / Struck, A.-W. / Thompson, M.L. / Menon, B. / Levy, C.W. / Leys, D. / Micklefield, J.
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 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_last ..._citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 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

Downloads & links

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Assembly

Deposited unit
A: Flavin-dependent tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1417
Polymers62,9371
Non-polymers1,2046
Water5,909328
1
A: Flavin-dependent tryptophan halogenase PrnA
hetero molecules

A: Flavin-dependent tryptophan halogenase PrnA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,28214
Polymers125,8742
Non-polymers2,40812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8510 Å2
ΔGint-118 kcal/mol
Surface area38720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.100, 68.100, 275.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Flavin-dependent tryptophan halogenase PrnA


Mass: 62937.055 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

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Non-polymers , 5 types, 334 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.54 Å3/Da / Density % sol: 51.51 %
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: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 27, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.204→68.84 Å / Num. obs: 33920 / % possible obs: 99.96 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.244 / Net I/σ(I): 8.3
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 13.4 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 3.8 / % 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: 2.204→68.84 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1719 5.07 %
Rwork0.1708 --
obs0.1731 33911 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.204→68.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4152 0 74 328 4554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024349
X-RAY DIFFRACTIONf_angle_d0.6715915
X-RAY DIFFRACTIONf_dihedral_angle_d11.9911577
X-RAY DIFFRACTIONf_chiral_restr0.033617
X-RAY DIFFRACTIONf_plane_restr0.003760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2044-2.26930.2641360.19712631X-RAY DIFFRACTION100
2.2693-2.34260.2471430.19042608X-RAY DIFFRACTION100
2.3426-2.42630.24521260.18632638X-RAY DIFFRACTION100
2.4263-2.52340.23661510.18532612X-RAY DIFFRACTION100
2.5234-2.63830.22961410.18032634X-RAY DIFFRACTION100
2.6383-2.77740.2341270.18492648X-RAY DIFFRACTION100
2.7774-2.95140.22541410.18682673X-RAY DIFFRACTION100
2.9514-3.17930.22591630.18122638X-RAY DIFFRACTION100
3.1793-3.49920.22131370.17632693X-RAY DIFFRACTION100
3.4992-4.00550.22471400.15412735X-RAY DIFFRACTION100
4.0055-5.04630.19131560.14092732X-RAY DIFFRACTION100
5.0463-68.87860.18921580.17442950X-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)
11.20950.48570.21172.4127-0.31280.58690.0140.01610.1767-0.2632-0.00920.2519-0.3827-0.40090.01180.37640.12360.00370.24460.02570.3003-42.2792-14.153-18.4664
20.4995-0.4096-0.24181.58860.39761.7397-0.0022-0.0152-0.0819-0.16860.0727-0.00370.16690.0706-0.07920.2449-0.00580.04490.1133-0.00830.2399-23.1365-40.6984-20.3371
31.1871-0.25320.01881.96620.48231.9092-0.00680.14510.2151-0.53940.02410.2049-0.8154-0.30680.02070.62210.18070.03520.20380.06280.2958-37.9715-7.7856-22.2643
41.28030.0818-0.71741.5662-1.00571.8831-0.11720.20130.0154-0.62950.1311-0.0205-0.1072-0.0052-0.0260.3710.00750.07210.1569-0.00440.2216-21.1028-25.9348-34.676
50.68110.1674-0.4820.8028-0.26411.60420.0145-0.02650.0351-0.16260.0363-0.1013-0.31470.0451-0.02750.3481-0.00150.06420.12510.00710.2673-23.1834-16.4198-18.6716
60.8288-1.48120.54642.9129-0.19452.0617-0.1121-0.204-0.10820.24790.23810.215-0.08710.0498-0.12320.23620.05260.06410.2062-0.0150.2509-18.5052-33.6795-7.134
73.4539-0.18753.71541.48790.00746.04490.0575-0.1356-0.2108-0.07080.03370.21530.4308-0.2107-0.09990.3577-0.01250.08970.16990.0050.3434-30.5723-49.1367-18.9839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 66 )
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 152 )
3X-RAY DIFFRACTION3chain 'A' and (resid 153 through 235 )
4X-RAY DIFFRACTION4chain 'A' and (resid 236 through 305 )
5X-RAY DIFFRACTION5chain 'A' and (resid 306 through 417 )
6X-RAY DIFFRACTION6chain 'A' and (resid 418 through 481 )
7X-RAY DIFFRACTION7chain 'A' and (resid 482 through 517 )

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