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- PDB-5b6i: Structure of fluorinase from Streptomyces sp. MA37 -

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Basic information

Entry
Database: PDB / ID: 5b6i
TitleStructure of fluorinase from Streptomyces sp. MA37
ComponentsFluorinase
KeywordsTRANSFERASE
Function / homology
Function and homology information


(R)-S-adenosyl-L-methionine hydrolase (adenosine-forming) / adenosyl-chloride synthase / adenosyl-fluoride synthase / adenosyl-fluoride synthase activity
Similarity search - Function
Adenosyl-fluoride synthase / Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain ...Adenosyl-fluoride synthase / Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / SAM hydroxide adenosyltransferase N-terminal domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE / METHIONINE / Fluorinase
Similarity search - Component
Biological speciesStreptomyces sp. MA37 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsXue, B. / Robinson, R.C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Directed Evolution of a Fluorinase for Improved Fluorination Efficiency with a Non-native Substrate
Authors: Sun, H. / Yeo, W.L. / Lim, Y.H. / Chew, X. / Smith, D.J. / Xue, B. / Chan, K.P. / Robinson, R.C. / Robins, E.G. / Zhao, H. / Ang, E.L.
History
DepositionMay 29, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fluorinase
B: Fluorinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5826
Polymers68,7492
Non-polymers8334
Water12,304683
1
A: Fluorinase
B: Fluorinase
hetero molecules

A: Fluorinase
B: Fluorinase
hetero molecules

A: Fluorinase
B: Fluorinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)208,74718
Polymers206,2486
Non-polymers2,49912
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
crystal symmetry operation10_554-y,z+1/2,-x-1/21
Buried area25830 Å2
ΔGint-119 kcal/mol
Surface area57850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.635, 125.635, 125.635
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-739-

HOH

21A-740-

HOH

31A-744-

HOH

41B-653-

HOH

51B-695-

HOH

61B-708-

HOH

71B-709-

HOH

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Components

#1: Protein Fluorinase /


Mass: 34374.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MA37 (bacteria) / Gene: flA1 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: W0W999
#2: Chemical ChemComp-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11NO2S
#3: Chemical ChemComp-ADN / ADENOSINE / Adenosine


Mass: 267.241 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C10H13N5O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 683 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Sodium acetate trihydrate, 30% v/v Polyethylene glycol 300

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.541 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Dec 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.8→39 Å / Num. obs: 60143 / % possible obs: 98.1 % / Redundancy: 8.78 % / Rsym value: 0.112 / Net I/σ(I): 19.7
Reflection shellResolution: 1.8→1.87 Å

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
SAINTdata reduction
PDB_EXTRACT3.11data extraction
SAINTdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RQP

1rqp


Resolution: 1.95→19.87 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20.81
RfactorNum. reflection% reflection
Rfree0.189 4592 4.94 %
Rwork0.162 --
obs0.163 48049 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.27 Å2
Refinement stepCycle: LAST / Resolution: 1.95→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 56 683 5141
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074609
X-RAY DIFFRACTIONf_angle_d1.1216288
X-RAY DIFFRACTIONf_dihedral_angle_d12.1041648
X-RAY DIFFRACTIONf_chiral_restr0.042712
X-RAY DIFFRACTIONf_plane_restr0.005817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9502-1.97240.2741680.23933013X-RAY DIFFRACTION100
1.9724-1.99560.26821510.22642950X-RAY DIFFRACTION100
1.9956-2.01990.24291660.21882959X-RAY DIFFRACTION100
2.0199-2.04540.29161760.21742849X-RAY DIFFRACTION100
2.0454-2.07230.29721400.21232917X-RAY DIFFRACTION99
2.0723-2.10070.2231620.21632967X-RAY DIFFRACTION100
2.1007-2.13060.26791940.2042890X-RAY DIFFRACTION99
2.1306-2.16240.22311260.20692982X-RAY DIFFRACTION100
2.1624-2.19610.2311440.19162978X-RAY DIFFRACTION100
2.1961-2.23210.22251440.1932940X-RAY DIFFRACTION99
2.2321-2.27050.20631500.18622927X-RAY DIFFRACTION100
2.2705-2.31180.21041260.17432991X-RAY DIFFRACTION99
2.3118-2.35620.24981400.17182887X-RAY DIFFRACTION99
2.3562-2.40420.22791180.1682974X-RAY DIFFRACTION99
2.4042-2.45640.20231380.16392981X-RAY DIFFRACTION99
2.4564-2.51340.22161520.16942960X-RAY DIFFRACTION99
2.5134-2.57610.26251300.16512900X-RAY DIFFRACTION99
2.5761-2.64560.21231220.15732967X-RAY DIFFRACTION100
2.6456-2.72330.19941740.15532974X-RAY DIFFRACTION100
2.7233-2.8110.18681220.15642942X-RAY DIFFRACTION100
2.811-2.91110.16331700.15162917X-RAY DIFFRACTION100
2.9111-3.02730.17871260.15012956X-RAY DIFFRACTION100
3.0273-3.16450.1811440.14682968X-RAY DIFFRACTION99
3.1645-3.33070.17671680.14322906X-RAY DIFFRACTION99
3.3307-3.53820.1532120.14312896X-RAY DIFFRACTION99
3.5382-3.80970.16231790.13282930X-RAY DIFFRACTION100
3.8097-4.18980.141610.1232929X-RAY DIFFRACTION100
4.1898-4.78860.12331560.11612968X-RAY DIFFRACTION100
4.7886-6.00540.1521840.14852907X-RAY DIFFRACTION100
6.0054-19.86570.1911490.18822973X-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)
10.4210.0408-0.090.1797-0.24240.3544-0.06120.057-0.03550.00070.01590.00990.0052-0.02170.00010.0493-0.00860.00690.06630.00580.063-2.989813.7176-47.1413
20.70380.29410.08840.9420.13270.5960.006-0.1322-0.06970.09060.0071-0.03380.06330.02290.00080.0530.0153-0.00080.07940.01860.05750.04075.198-36.9078
30.26130.6680.43972.03361.13630.7387-0.0635-0.8327-0.37320.7372-0.04910.82340.4621-0.4577-0.12920.44650.00240.15760.57530.16270.5535-11.5012.19-17.669
40.64990.2579-0.34980.77690.30060.9695-0.027-0.1272-0.12180.1216-0.0066-0.00980.12420.0229-00.12240.00970.03470.13620.02650.1086-27.4426-0.0565-26.068
50.5463-0.2590.05550.36150.22840.38330.0475-0.09750.07610.1127-0.01090.0955-0.0658-0.0495-0.00070.13460.00310.0330.12430.01170.0952-25.770310.0979-26.3739
60.39070.0890.07530.1111-0.16110.36620.0367-0.09350.07550.02610.03790.0612-0.0447-0.1475-00.11260.00480.01470.14380.00840.1164-48.447740.9216-8.1958
70.48220.1182-0.17691.1653-0.37050.8873-0.0184-0.16110.02720.2267-0.0253-0.0433-0.11630.0819-0.00040.1665-0.0181-0.01040.16510.00160.0919-39.355741.66541.4999
80.11480.0846-0.05760.1251-0.08470.0544-0.25920.0709-0.0643-0.0487-0.0688-0.4128-0.18410.1884-0.00120.3444-0.0352-0.03590.37020.13010.3304-16.599339.1583-1.6426
91.06110.3148-0.1661.1015-0.13910.46120.0047-0.1263-0.11670.1411-0.0289-0.07980.02940.030600.1298-0.02340.00720.1194-0.01150.133-15.439848.909-16.5344
100.2645-0.36570.01980.6737-0.06360.812-0.08990.0951-0.2184-0.09370.0025-0.27930.09670.1337-0.00750.1403-0.01-0.00080.1304-0.0060.2032-19.357940.2556-19.498
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 34 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 35 THROUGH 186 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 187 THROUGH 200 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 201 THROUGH 277 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 278 THROUGH 302 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 8 THROUGH 34 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 35 THROUGH 186 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 187 THROUGH 200 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 201 THROUGH 277 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 278 THROUGH 302 )

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