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- PDB-2v7v: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from ... -

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Basic information

Entry
Database: PDB / ID: 2v7v
TitleX-ray crystal structure of 5'-fluorodeoxyadenosine synthase from streptomyces cattleya complexed with 5'-fluorodeoxyadenosine
Components5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
KeywordsTRANSFERASE / MECHANISM OF 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: 1.94 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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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 "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)98,0126
Polymers97,2043
Non-polymers8083
Water13,043724
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)196,02412
Polymers194,4096
Non-polymers1,6156
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area22470 Å2
ΔGint-157.5 kcal/mol
Surface area77260 Å2
MethodPQS
Unit cell
Length a, b, c (Å)75.892, 129.946, 184.491
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
11ARGARGALAALAAA8 - 948 - 94
21ARGARGALAALABB8 - 948 - 94
31ARGARGALAALACC8 - 948 - 94
12TRPTRPARGARGAA103 - 192103 - 192
22TRPTRPARGARGBB103 - 192103 - 192
32TRPTRPARGARGCC103 - 192103 - 192
13LEULEUILEILEAA202 - 220202 - 220
23LEULEUILEILEBB202 - 220202 - 220
33LEULEUILEILECC202 - 220202 - 220
14GLYGLYLEULEUAA231 - 240231 - 240
24GLYGLYLEULEUBB231 - 240231 - 240
34GLYGLYLEULEUCC231 - 240231 - 240
15GLUGLUALAALAAA247 - 298247 - 298
25GLUGLUALAALABB247 - 298247 - 298
35GLUGLUALAALACC247 - 298247 - 298

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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 genetically manipulated source
Source: (gene. exp.) STREPTOMYCES CATTLEYA (bacteria) / Plasmid: PEHISTEV-FLA / 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.: 724 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: pH 4.6

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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→37.2 Å / Num. obs: 61281 / % possible obs: 95.5 % / Observed criterion σ(I): 6 / Redundancy: 5.2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 25
Reflection shellResolution: 1.9→2 Å / Redundancy: 5 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 6 / % possible all: 90.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RQP

1rqp


Resolution: 1.94→37.16 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.481 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.177 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3194 5 %RANDOM
Rwork0.18 ---
obs0.182 61281 95.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å20 Å20 Å2
2---0.92 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 1.94→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 57 724 7441
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226930
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9719467
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9265878
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91622.957301
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.367151026
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1291555
X-RAY DIFFRACTIONr_chiral_restr0.0890.21054
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025383
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.23305
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.24709
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2580.2100
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7321.54493
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.18327025
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.70932831
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7394.52439
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
1A1026tight positional0.050.05
2B1026tight positional0.090.05
3C1026tight positional0.110.05
1A929medium positional0.410.5
2B929medium positional0.510.5
3C929medium positional0.490.5
1A1026tight thermal0.150.5
2B1026tight thermal0.140.5
3C1026tight thermal0.160.5
1A929medium thermal0.732
2B929medium thermal0.772
3C929medium thermal0.862
LS refinement shellResolution: 1.94→1.99 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.283 206
Rwork0.212 4338
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)
11.0905-0.3392-0.17310.49610.07940.54340.02670.1007-0.1584-0.0088-0.08170.11310.0582-0.10860.055-0.0555-0.02110.0042-0.0319-0.0195-0.042522.494614.372469.0275
20.66040.14420.41550.40150.3380.7772-0.044-0.01760.1364-0.0345-0.02370.0811-0.2061-0.02560.06770.01150.0132-0.0056-0.05330.0062-0.026327.403945.77270.0207
30.17770.14550.11620.7394-0.05810.6596-0.01510.0014-0.0630.00480.0112-0.19430.00370.11870.004-0.0519-0.0057-0.0132-0.01880.0043-0.000951.642225.61973.8626
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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