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- PDB-1rqr: Crystal structure and mechanism of a bacterial fluorinating enzym... -

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Basic information

Entry
Database: PDB / ID: 1rqr
TitleCrystal structure and mechanism of a bacterial fluorinating enzyme, product complex
Components5'-fluoro-5'-deoxyadenosine synthase
KeywordsTRANSFERASE / fluorinase / central 7 stranded beta sheets / anti-parallel beta sheets
Function / homology
Function and homology information


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 / 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
5'-FLUORO-5'-DEOXYADENOSINE / METHIONINE / Fluorinase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsDong, C. / Huang, F. / Deng, H. / Schaffrath, C. / Spencer, J.B. / O'Hagan, D. / Naismith, J.H.
Citation
Journal: Nature / Year: 2004
Title: Crystal structure and mechanism of a bacterial fluorinating enzyme
Authors: Dong, C. / Huang, F. / Deng, H. / Schaffrath, C. / Spencer, J.B. / O'Hagan, D. / Naismith, J.H.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2003
Title: Crystallization and X-ray diffraction of 5'-fluoro-5'-deoxyadenosine synthase, a fluorination enzyme from Streptomyces cattleya
Authors: Dong, C.J. / Deng, H. / Dorward, M. / Schaffrath, C. / O'Hagan, D. / Naismith, J.H.
History
DepositionDec 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jun 15, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5'-fluoro-5'-deoxyadenosine synthase
B: 5'-fluoro-5'-deoxyadenosine synthase
C: 5'-fluoro-5'-deoxyadenosine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,3049
Polymers98,0493
Non-polymers1,2556
Water2,864159
1
A: 5'-fluoro-5'-deoxyadenosine synthase
B: 5'-fluoro-5'-deoxyadenosine synthase
C: 5'-fluoro-5'-deoxyadenosine synthase
hetero molecules

A: 5'-fluoro-5'-deoxyadenosine synthase
B: 5'-fluoro-5'-deoxyadenosine synthase
C: 5'-fluoro-5'-deoxyadenosine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,60818
Polymers196,0976
Non-polymers2,51112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_456x-1/2,-y+1/2,-z+11
2
A: 5'-fluoro-5'-deoxyadenosine synthase
B: 5'-fluoro-5'-deoxyadenosine synthase
C: 5'-fluoro-5'-deoxyadenosine synthase
hetero molecules

A: 5'-fluoro-5'-deoxyadenosine synthase
B: 5'-fluoro-5'-deoxyadenosine synthase
C: 5'-fluoro-5'-deoxyadenosine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,60818
Polymers196,0976
Non-polymers2,51112
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area26770 Å2
ΔGint-110 kcal/mol
Surface area59110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)76.184, 129.923, 183.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a hexamer generated from the trimer in the asymmetric unit

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Components

#1: Protein 5'-fluoro-5'-deoxyadenosine synthase


Mass: 32682.861 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cattleya (bacteria) / Gene: fla / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q70GK9, adenosyl-fluoride synthase
#2: Chemical ChemComp-5FD / 5'-FLUORO-5'-DEOXYADENOSINE


Mass: 269.232 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12FN5O3
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 22% PEG 1000, 0.1M phosphate-citrate, 0.2M Li2SO4, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 293 K / pH: 7.8 / Method: vapor diffusion, sitting drop
Details: Dong, C., (2003) Acta Crystallogr.,Sect.D, 59, 2292.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
122 %PEG10001reservoir
20.1 Mphosphate-citrate1reservoirpH4.2
30.2 M1reservoirLi2SO4
425 mMTris-HCl1droppH7.8
55 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9786 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 8, 2003 / Details: 2 Mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.67→53.64 Å / Num. all: 26303 / Num. obs: 26003 / % possible obs: 99 % / Observed criterion σ(F): 5.967 / Observed criterion σ(I): 5.4 / Redundancy: 6.3 % / Biso Wilson estimate: 47.6 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.064 / Net I/σ(I): 3
Reflection shellResolution: 2.67→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 5.4 / Num. unique all: 1821 / Rsym value: 0.133 / % possible all: 99
Reflection
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 53 Å / Num. obs: 26303 / % possible obs: 97 % / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 81 % / Rmerge(I) obs: 0.13 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→91.29 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 10.333 / SU ML: 0.219 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 5.96 / σ(I): 3.5 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 1322 5.1 %RANDOM
Rwork0.17329 ---
all0.231 26303 --
obs0.17627 24648 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.058 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å20 Å20 Å2
2---0.26 Å20 Å2
3----0.77 Å2
Refine analyzeLuzzati coordinate error obs: 0.17 Å
Refinement stepCycle: LAST / Resolution: 2.67→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 84 159 6903
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216915
X-RAY DIFFRACTIONr_bond_other_d0.0030.026225
X-RAY DIFFRACTIONr_angle_refined_deg1.3781.9749438
X-RAY DIFFRACTIONr_angle_other_deg0.856314400
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.515870
X-RAY DIFFRACTIONr_chiral_restr0.0720.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027770
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021440
X-RAY DIFFRACTIONr_nbd_refined0.190.21380
X-RAY DIFFRACTIONr_nbd_other0.2350.27792
X-RAY DIFFRACTIONr_nbtor_other0.1040.23926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2197
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2080.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.25
X-RAY DIFFRACTIONr_mcbond_it0.4751.54356
X-RAY DIFFRACTIONr_mcangle_it0.90127017
X-RAY DIFFRACTIONr_scbond_it1.33432559
X-RAY DIFFRACTIONr_scangle_it2.2174.52421
LS refinement shellResolution: 2.67→2.742 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 96 -
Rwork0.216 1724 -
obs-1821 95.5 %
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)
11.3336-0.1319-0.2390.3580.09610.5487-0.00150.0635-0.17130.0232-0.0850.06190.0344-0.13960.08650.0349-0.02120.0290.0692-0.01740.093122.59314.03868.794
20.93520.1860.42190.58180.3520.7933-0.0302-0.01340.1051-0.0272-0.02910.0732-0.2191-0.00880.05930.10640.01070.00450.0314-0.00850.072127.21545.66569.601
30.39320.0844-0.01530.5863-0.11240.6655-0.0079-0.0357-0.03880.043-0.0088-0.0891-0.01290.110.01680.06850.001-0.01460.07950.01010.085151.82125.72573.641
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 2988 - 298
2X-RAY DIFFRACTION2BB8 - 2988 - 298
3X-RAY DIFFRACTION3CC8 - 2988 - 298
Refinement
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 53 Å / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.014
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.34
LS refinement shell
*PLUS
Lowest resolution: 2.74 Å

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