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- PDB-5lmz: Fluorinase from Streptomyces sp. MA37 -

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Basic information

Entry
Database: PDB / ID: 5lmz
TitleFluorinase from Streptomyces sp. MA37
ComponentsFluorinase
KeywordsTRANSFERASE / Fluorinase
Function / homology
Function and homology information


(R)-S-adenosyl-L-methionine hydrolase (adenosine-forming) / adenosyl-chloride synthase / adenosyl-fluoride synthase / adenosyl-fluoride synthase activity / hydrolase 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 / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain superfamily / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-terminal domain ...Adenosyl-fluoride synthase / Bacterial fluorinating enzyme like / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal / 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 / S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal domain / S-adenosyl-l-methionine hydroxide adenosyltransferase, C-terminal domain / SAM hydroxide adenosyltransferase N-terminal domain / SAM hydroxide adenosyltransferase C-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
1-DEAZA-ADENOSINE / Fluorinase
Similarity search - Component
Biological speciesStreptomyces sp. MA37 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMann, G. / O'Hagan, D. / Naismith, J.H. / Bandaranayaka, N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
ERC Advanced Grant United Kingdom
CitationJournal: Chembiochem / Year: 2014
Title: Identification of fluorinases from Streptomyces sp MA37, Norcardia brasiliensis, and Actinoplanes sp N902-109 by genome mining.
Authors: Deng, H. / Ma, L. / Bandaranayaka, N. / Qin, Z. / Mann, G. / Kyeremeh, K. / Yu, Y. / Shepherd, T. / Naismith, J.H. / O'Hagan, D.
History
DepositionAug 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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: Fluorinase
B: Fluorinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6849
Polymers64,8612
Non-polymers8237
Water4,071226
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)197,05327
Polymers194,5846
Non-polymers2,46921
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 area27760 Å2
ΔGint-224 kcal/mol
Surface area57450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.920, 125.920, 125.920
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
11B-500-

HOH

21B-507-

HOH

31B-509-

HOH

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Components

#1: Protein Fluorinase


Mass: 32430.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. MA37 (bacteria) / Gene: flA1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: W0W999
#2: Chemical ChemComp-1DA / 1-DEAZA-ADENOSINE


Mass: 266.253 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N4O4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / 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: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.5 M NaCl, 7 % w/v PEG6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.55→18.17 Å / Num. obs: 21982 / % possible obs: 99.7 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.2 / Net I/σ(I): 11.4
Reflection shellResolution: 2.55→2.69 Å / Redundancy: 11.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2C2W

2c2w


Resolution: 2.55→18.17 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.22
RfactorNum. reflection% reflection
Rfree0.2158 1123 5.13 %
Rwork0.166 --
obs0.1686 21905 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 35.76 Å2
Refinement stepCycle: LAST / Resolution: 2.55→18.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4304 0 53 226 4583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074483
X-RAY DIFFRACTIONf_angle_d0.9786122
X-RAY DIFFRACTIONf_dihedral_angle_d12.311586
X-RAY DIFFRACTIONf_chiral_restr0.052698
X-RAY DIFFRACTIONf_plane_restr0.005789
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5502-2.66590.27451400.20582557X-RAY DIFFRACTION100
2.6659-2.8060.27091380.20082584X-RAY DIFFRACTION100
2.806-2.98110.27221460.2022542X-RAY DIFFRACTION100
2.9811-3.21010.24211360.18612598X-RAY DIFFRACTION100
3.2101-3.5310.23881550.16932568X-RAY DIFFRACTION100
3.531-4.03710.18321180.14542620X-RAY DIFFRACTION100
4.0371-5.0680.17081500.1312607X-RAY DIFFRACTION100
5.068-18.17540.19251400.16652706X-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)
13.3232-0.1393-1.01852.6489-0.01292.78440.0941-0.0810.1082-0.0380.0021-0.0242-0.31360.1467-0.02780.1732-0.0213-0.00730.199-0.00890.1788-2.849913.5848-47.2283
22.41630.4454-0.2671.85450.36831.7354-0.0761-0.3386-0.08050.14630.0876-0.13870.11430.1955-0.0130.16820.06480.00360.24870.01180.16590.45265.5151-37.206
31.4023-0.6677-0.4050.59510.27250.07970.0399-0.6269-0.53330.1044-0.05660.37490.44440.34080.02080.34170.13750.09840.51290.16950.4241-17.86871.9914-24.5008
41.88890.2987-0.28542.05530.08232.4847-0.2252-0.4496-0.43210.1913-0.0815-0.0490.50330.10650.22220.31370.05130.11240.30990.08120.2879-30.51822.4192-26.5451
52.98580.0098-0.7691.36140.02093.02260.03640.05560.1170.0557-0.00210.2669-0.0858-0.3766-0.09420.22380.02830.02640.23490.01950.2308-48.342542.687-7.8529
60.7684-0.71840.08493.18330.15792.2672-0.0482-0.21660.13150.08330.1348-0.2463-0.12830.2589-0.12030.2786-0.0033-0.02850.3022-0.02370.2042-35.486443.3744-2.6536
71.82990.5675-0.30311.4461-0.10981.28570.0311-0.37370.09120.4908-0.05040.079-0.16770.21020.06270.3599-0.0179-0.02340.28710.02030.1467-37.782240.09554.2957
82.4915-0.12110.44843.5146-0.47721.6970.0278-0.05230.1180.22790.0456-0.1524-0.01110.2359-0.04660.1902-0.04090.02780.2524-0.03630.2337-16.103847.218-17.9436
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 228 )
4X-RAY DIFFRACTION4chain 'A' and (resid 229 through 298 )
5X-RAY DIFFRACTION5chain 'B' and (resid 8 through 44 )
6X-RAY DIFFRACTION6chain 'B' and (resid 45 through 107 )
7X-RAY DIFFRACTION7chain 'B' and (resid 108 through 201 )
8X-RAY DIFFRACTION8chain 'B' and (resid 202 through 298 )

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