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- PDB-2v7w: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g... -

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Basic information

Entry
Database: PDB / ID: 2v7w
TitleX-ray crystal structure of 5'-fluorodeoxyadenosine synthase s158g mutant complexed with 5'-fluorodeoxyadenosin
Components5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
KeywordsTRANSFERASE / FLUORINATION / BIOSYNTHETIC PROTEIN
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 / Fluorinase
Similarity search - Component
Biological speciesSTREPTOMYCES CATTLEYA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhu, X. / O'Hagan, D. / Naismith, J.H.
CitationJournal: J. Am. Chem. Soc. / Year: 2007
Title: Mechanism of enzymatic fluorination in Streptomyces cattleya.
Authors: Zhu, X. / Robinson, D.A. / McEwan, A.R. / O'Hagan, D. / Naismith, J.H.
History
DepositionAug 2, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 2.0Jul 13, 2022Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Other / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_database_status / pdbx_validate_chiral
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 / _pdbx_database_status.status_code_sf
Revision 2.1Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB", "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)97,9226
Polymers97,1143
Non-polymers8083
Water10,539585
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)195,84412
Polymers194,2296
Non-polymers1,6156
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area22800 Å2
ΔGint-188.3 kcal/mol
Surface area76440 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.854, 129.256, 184.485
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROALAALAAA9 - 949 - 94
21PROPROALAALABB9 - 949 - 94
31PROPROALAALACC9 - 949 - 94
12TRPTRPARGARGAA103 - 192103 - 192
22TRPTRPARGARGBB103 - 192103 - 192
32TRPTRPARGARGCC103 - 192103 - 192
13VALVALILEILEAA203 - 220203 - 220
23VALVALILEILEBB203 - 220203 - 220
33VALVALILEILECC203 - 220203 - 220
14GLYGLYASPASPAA231 - 241231 - 241
24GLYGLYASPASPBB231 - 241231 - 241
34GLYGLYASPASPCC231 - 241231 - 241
15GLUGLUALAALAAA247 - 298247 - 298
25GLUGLUALAALABB247 - 298247 - 298
35GLUGLUALAALACC247 - 298247 - 298

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Components

#1: Protein 5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE / 5'-FLUORO-5'-DEOXY ADENOSINE SYNTHETASE


Mass: 32371.467 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CATTLEYA (bacteria) / Plasmid: PEHISTEV-FLAS158G / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 158 TO GLY ENGINEERED RESIDUE IN CHAIN B, SER 158 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, SER 158 TO GLY ENGINEERED RESIDUE IN CHAIN B, SER 158 TO GLY ENGINEERED RESIDUE IN CHAIN C, SER 158 TO GLY
Has protein modificationN
Sequence detailsSITE DIRECTED MUTAGENESIS

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 4.6
Details: 0.1M CITRATE-PHOSPHATE BUFFER PH4.6, 20%PEG1000, 0.2M LI2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: May 8, 2006 / Details: TOROIDAL MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.9→53.4 Å / Num. obs: 67279 / % possible obs: 99 % / Observed criterion σ(I): 4 / Redundancy: 6.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 4 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RQP

1rqp


Resolution: 1.9→53.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.989 / SU ML: 0.092 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3535 5 %RANDOM
Rwork0.187 ---
obs0.189 67279 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.61 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.9→53.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6654 0 57 585 7296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226891
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3911.9719412
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615872
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.37123.154298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.444151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1871551
X-RAY DIFFRACTIONr_chiral_restr0.0890.21048
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025351
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1950.23264
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24669
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2528
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.2103
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8191.54481
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27626993
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.85732807
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9264.52418
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1027tight positional0.060.05
2B1027tight positional0.090.05
3C1027tight positional0.110.05
1A937medium positional0.280.5
2B937medium positional0.340.5
3C937medium positional0.370.5
1A1027tight thermal0.160.5
2B1027tight thermal0.150.5
3C1027tight thermal0.170.5
1A937medium thermal0.782
2B937medium thermal0.772
3C937medium thermal0.932
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.274 237
Rwork0.218 4656
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)
11.131-0.2812-0.18260.64260.16260.52040.02060.1303-0.1568-0.0343-0.05620.13310.0605-0.09830.0357-0.0424-0.0251-0.002-0.038-0.0194-0.059722.446714.207769.026
20.75690.120.55320.42920.37470.9505-0.05170.00150.1531-0.0469-0.02180.0749-0.1975-0.00830.0735-0.0050.0040.0016-0.05890.0163-0.0327.354145.586670.0077
30.33810.11830.09230.696-0.05250.6561-0.00960.0409-0.064-0.00690.0098-0.18580.01950.123-0.0002-0.0424-0.0049-0.0112-0.0204-0.006-0.025251.638325.457273.8386
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 298
2X-RAY DIFFRACTION2B8 - 298
3X-RAY DIFFRACTION3C8 - 298

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