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- PDB-2c5h: X-ray crystal structure of 5'-fluorodeoxyadenosine synthase from ... -

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Basic information

Entry
Database: PDB / ID: 2c5h
TitleX-ray crystal structure of 5'-fluorodeoxyadenosine synthase from Streptomyces cattleya complexed with 2'deoxy-adenosine
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
Chem-3D1 / METHIONINE / Fluorinase
Similarity search - Component
Biological speciesSTREPTOMYCES CATTLEYA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMcEwan, A.R. / Deng, H. / McGlinchey, R.P. / Robinson, D.R. / O'Hagan, D. / Naismith, J.H. / Spencer, J.
CitationJournal: To be Published
Title: Substrates and Inhibitors of the Fluorinase from Streptomyces Cattleya
Authors: Mcewan, A.R. / Deng, H. / Mcglinchey, R.P. / Robinson, D.R. / O'Hagan, D. / Naismith, J.H.
History
DepositionOct 27, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 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 BB CB" IN EACH CHAIN ON SHEET RECORDS ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB BB 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)98,2929
Polymers97,2043
Non-polymers1,0886
Water1,72996
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)196,58418
Polymers194,4096
Non-polymers2,17512
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)74.543, 126.697, 181.333
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
11B
21C
31A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 10 - 288 / Label seq-ID: 10 - 288

Dom-IDAuth asym-IDLabel asym-ID
1BB
2CC
3AA

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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 BL21(DE3) (bacteria) / References: UniProt: Q70GK9, adenosyl-fluoride synthase
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical ChemComp-3D1 / (2R,3S,5R)-5-(6-amino-9H-purin-9-yl)-tetrahydro-2-(hydroxymethyl)furan-3-ol / 2'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.23 Å3/Da / Density % sol: 44.8 %
Crystal growpH: 4
Details: 32%PEG 1K, 100MM PHOSPHATE CITRATE PH4.2, 200MM LI2SO4, pH 4.00

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 16, 2005 / Details: MIRROR
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.7→59.76 Å / Num. obs: 22733 / % possible obs: 94.9 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / % possible all: 97.2

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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: 2.7→50 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.857 / SU B: 37.18 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.462 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 1146 5 %RANDOM
Rwork0.228 ---
obs0.231 21556 94.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.02 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å20 Å20 Å2
2---4.88 Å20 Å2
3---3.61 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6660 0 73 96 6829
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226904
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5841.9729423
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8995870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54723.131297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.167151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9531551
X-RAY DIFFRACTIONr_chiral_restr0.0990.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025351
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.23794
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.24755
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2347
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3220.2114
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6021.54445
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01127010
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.63432810
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3974.52413
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
1B1116tight positional0.070.05
2C1116tight positional0.070.05
3A1116tight positional0.050.05
1B1013medium positional0.480.5
2C1013medium positional0.520.5
3A1013medium positional0.40.5
1B1116tight thermal0.070.5
2C1116tight thermal0.070.5
3A1116tight thermal0.060.5
1B1013medium thermal0.592
2C1013medium thermal0.592
3A1013medium thermal0.572
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.519 77
Rwork0.391 1602
Refinement TLS params.Method: refined / Origin x: 4.276 Å / Origin y: 36.376 Å / Origin z: -20.83 Å
111213212223313233
T-0.394 Å2-0.0076 Å2-0.0157 Å2-0.1938 Å20.0056 Å2---0.4817 Å2
L1.1312 °2-0.0291 °2-0.1328 °2-1.1429 °2-0.1898 °2--1.1616 °2
S-0.0414 Å °0.0128 Å °0.0393 Å °0.0415 Å °-0.0466 Å °-0.0022 Å °0.0674 Å °-0.0001 Å °0.088 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 290
2X-RAY DIFFRACTION1B10 - 290
3X-RAY DIFFRACTION1C10 - 290

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