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- PDB-1rqp: Crystal structure and mechanism of a bacterial fluorinating enzyme -

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Basic information

Entry
Database: PDB / ID: 1rqp
TitleCrystal structure and mechanism of a bacterial fluorinating enzyme
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, 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
S-ADENOSYLMETHIONINE / Fluorinase
Similarity search - Component
Biological speciesStreptomyces cattleya (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 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. / Deng, H. / Dorward, M. / Schaffrath, C. / O'Hagan, D. / Naismith, J.H.
History
DepositionDec 6, 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: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)98,4006
Polymers97,2043
Non-polymers1,1953
Water12,953719
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)196,80012
Polymers194,4096
Non-polymers2,3916
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)196,80012
Polymers194,4096
Non-polymers2,3916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area23500 Å2
ΔGint-111 kcal/mol
Surface area59210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.908, 130.302, 183.435
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-573-

HOH

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: 32401.490 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Streptomyces cattleya (bacteria) / Strain: NRRL8057 / References: UniProt: Q70GK9, adenosyl-fluoride synthase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.33 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 22% PEG 1000, 0.1 M phosphate-citrate, 0.2 M 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: ID14-2 / Wavelength: 0.933, 0.9786, 0.9783, 0.8984
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2002 / Details: Toroidal Zerodur mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.97861
30.97831
40.89841
ReflectionResolution: 1.8→65 Å / Num. all: 84305 / Num. obs: 80164 / % possible obs: 94 % / Observed criterion σ(F): 1.33 / Observed criterion σ(I): 1.5 / Redundancy: 10 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.11 / Rsym value: 0.12 / Net I/σ(I): 2.8
Reflection shellResolution: 1.8→1.847 Å / Redundancy: 6 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1100 / Rsym value: 0.5 / % possible all: 70
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 65 Å / Num. obs: 67204 / Redundancy: 4.8 % / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.98 Å / % possible obs: 93 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→91.29 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.907 / SU ML: 0.089 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 1.3 / ESU R: 0.283 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21669 3991 5 %RANDOM
Rwork0.16712 ---
all0.17 84305 --
obs0.16962 76173 95.09 %-
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: 16.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.8→91.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 81 719 7460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0216915
X-RAY DIFFRACTIONr_bond_other_d0.0020.026183
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9669444
X-RAY DIFFRACTIONr_angle_other_deg0.985314319
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7175870
X-RAY DIFFRACTIONr_chiral_restr0.0980.21053
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027797
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021425
X-RAY DIFFRACTIONr_nbd_refined0.2140.21397
X-RAY DIFFRACTIONr_nbd_other0.2530.27905
X-RAY DIFFRACTIONr_nbtor_other0.0850.23910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2552
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.330.232
X-RAY DIFFRACTIONr_symmetry_vdw_other0.310.2117
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2420.229
X-RAY DIFFRACTIONr_mcbond_it1.1111.54356
X-RAY DIFFRACTIONr_mcangle_it1.71227017
X-RAY DIFFRACTIONr_scbond_it2.45632559
X-RAY DIFFRACTIONr_scangle_it3.7194.52427
X-RAY DIFFRACTIONr_rigid_bond_restr1.43126915
X-RAY DIFFRACTIONr_sphericity_free4.1312719
X-RAY DIFFRACTIONr_sphericity_bonded1.89526741
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 278
Rwork0.229 5478
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)
10.9413-0.1215-0.2010.38450.07140.3934-0.03230.0846-0.15760.0158-0.05380.07540.0394-0.11260.08610.0227-0.01590.02060.0501-0.02660.061722.50114.16668.629
20.56590.12190.24660.30340.23550.6453-0.0342-0.01450.1276-0.0392-0.03430.0433-0.1991-0.0170.06850.08670.0236-0.0110.0185-0.01180.051827.09445.74569.441
30.39660.15-0.00620.26050.05440.64170.0013-0.0361-0.07170.0196-0.011-0.0917-0.04770.10310.00970.04270.0036-0.01540.04630.01430.05251.64125.74673.445
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 2978 - 297
2X-RAY DIFFRACTION2BB8 - 2978 - 297
3X-RAY DIFFRACTION3CC8 - 2978 - 297
Refinement
*PLUS
Highest resolution: 19 Å / Lowest resolution: 65 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.167
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.65
LS refinement shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 1.98 Å

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