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- PDB-2c5b: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from ... -

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Basic information

Entry
Database: PDB / ID: 2c5b
TitleX-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 2'deoxy-5'deoxy-fluoroadenosine.
Components5'-FLUORO-5'-DEOXYADENOSINE SYNTHASE
KeywordsTRANSFERASE / FLUORINASE / 5'-FLUORODEOXYADENOSINE SYNTHASE / FLA / INHIBITOR / AZA / STREPTOMYCES CATTLEYA / SAM ANALOGUE
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-2',5'-DIDEOXYADENOSINE / METHIONINE / Fluorinase
Similarity search - Component
Biological speciesSTREPTOMYCES CATTLEYA (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMcEwan, A.R. / Deng, H. / McGlinchey, R.P. / Robinson, D.A. / O'Hagan, D. / Naismith, J.H. / Spencer, J.
CitationJournal: Org.Biomol.Chem. / Year: 2006
Title: Substrate Specificity in Enzymatic Fluorination. The Fluorinase from Streptomyces Cattleya Accepts 2'-Deoxyadenosine Substrates.
Authors: Cobb, S.L. / Deng, H. / Mcewan, A.R. / Naismith, J.H. / O'Hagan, D. / Robinson, D.A.
History
DepositionOct 26, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)98,4129
Polymers97,2043
Non-polymers1,2076
Water3,531196
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)196,82418
Polymers194,4096
Non-polymers2,41512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
MethodPQS
Unit cell
Length a, b, c (Å)76.153, 129.669, 183.165
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
12B
22C
13C
23A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 20 - 270 / Label seq-ID: 20 - 270

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12BB
22CC
13CC
23AA

NCS ensembles :
ID
1
2
3

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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 / Variant (production host): DE3 / References: UniProt: Q70GK9, adenosyl-fluoride synthase
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-5F1 / 5'-FLUORO-2',5'-DIDEOXYADENOSINE


Mass: 253.233 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12FN5O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.37 Å3/Da / Density % sol: 49 %
Crystal growpH: 4
Details: 32%PEG 1K, 100MM PHOSPHATECITRATE PH4.2, 200MM LI2SO4, pH 4.00

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RAXIS / Detector: IMAGE PLATE / Date: May 17, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→37.69 Å / Num. obs: 27454 / % possible obs: 87 % / Observed criterion σ(I): 3 / Redundancy: 2.9 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 7.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3.4 / % possible all: 88

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RQP

1rqp


Resolution: 2.5→37 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.864 / SU B: 19.697 / SU ML: 0.246 / Cross valid method: THROUGHOUT / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1344 4.9 %RANDOM
Rwork0.189 ---
obs0.193 26074 86.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2---1.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 81 196 6937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226912
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9729432
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2165870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.87823.131297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.246151023
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3291551
X-RAY DIFFRACTIONr_chiral_restr0.0890.21050
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025355
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.23476
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24670
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2338
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.282
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0420.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.54457
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.77427017
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.19132815
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8864.52415
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

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1004medium positional0.180.5
2B1004medium positional0.260.5
3C1004medium positional0.190.5
1A912loose positional0.475
2B912loose positional0.55
3C912loose positional0.485
1A1004medium thermal0.422
2B1004medium thermal0.422
3C1004medium thermal0.452
1A912loose thermal1.1110
2B912loose thermal1.1310
3C912loose thermal1.1410
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 105 -
Rwork0.249 1898 -
obs--87.35 %

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