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- PDB-6rz2: SalL with Chloroadenosine -

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Basic information

Entry
Database: PDB / ID: 6rz2
TitleSalL with Chloroadenosine
ComponentsAdenosyl-chloride synthase
KeywordsTRANSFERASE / SalL / chloroadenosine / chlorinase
Function / homology
Function and homology information


adenosyl-chloride synthase / transferase activity, transferring alkyl or aryl (other than methyl) groups
Similarity search - Function
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
Similarity search - Domain/homology
5'-CHLORO-5'-DEOXYADENOSINE / Adenosyl-chloride synthase
Similarity search - Component
Biological speciesSalinispora tropica CNB-440 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsMcKean, I. / Frese, A. / Cuetos, A. / Burley, G. / Grogan, G.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2019
Title: S-Adenosyl Methionine Cofactor Modifications Enhance the Biocatalytic Repertoire of Small Molecule C-Alkylation.
Authors: McKean, I.J.W. / Sadler, J.C. / Cuetos, A. / Frese, A. / Humphreys, L.D. / Grogan, G. / Hoskisson, P.A. / Burley, G.A.
History
DepositionJun 12, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine / refine_hist / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _refine_hist.d_res_low / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosyl-chloride synthase
B: Adenosyl-chloride synthase
C: Adenosyl-chloride synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,3836
Polymers90,5263
Non-polymers8573
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8740 Å2
ΔGint-53 kcal/mol
Surface area29550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.842, 111.579, 165.565
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA2 - 2712 - 271
21PROPROBB2 - 2712 - 271
12SERSERAA2 - 2702 - 270
22SERSERCC2 - 2702 - 270
13ARGARGBB2 - 2722 - 272
23ARGARGCC2 - 2722 - 272

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Adenosyl-chloride synthase / 5'-chloro-5'-deoxyadenosine synthase / Chlorinase SalL


Mass: 30175.256 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinispora tropica CNB-440 (bacteria) / Gene: salL, Strop_1026 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4X3Q0, adenosyl-chloride synthase
#2: Chemical ChemComp-5CD / 5'-CHLORO-5'-DEOXYADENOSINE


Mass: 285.687 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H12ClN5O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.1 M HEPES pH 7; 20% PEG 6000; 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97623 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97623 Å / Relative weight: 1
ReflectionResolution: 1.77→49.47 Å / Num. obs: 92806 / % possible obs: 100 % / Redundancy: 8 % / Biso Wilson estimate: 18 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.05 / Net I/σ(I): 15.7
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 4561 / CC1/2: 0.83 / Rpim(I) all: 0.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q6I

2q6i


Resolution: 1.77→49.47 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.3 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20148 4527 4.9 %RANDOM
Rwork0.1707 ---
obs0.17219 88185 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.511 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å2-0 Å2-0 Å2
2---1.25 Å20 Å2
3---1.66 Å2
Refinement stepCycle: LAST / Resolution: 1.77→49.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5952 0 57 693 6702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0136175
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175682
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.6488473
X-RAY DIFFRACTIONr_angle_other_deg1.4391.57113150
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3965803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83822.895266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43615872
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1081527
X-RAY DIFFRACTIONr_chiral_restr0.0880.2845
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.026960
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021210
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2022.453209
X-RAY DIFFRACTIONr_mcbond_other2.22.4493208
X-RAY DIFFRACTIONr_mcangle_it3.1393.6534001
X-RAY DIFFRACTIONr_mcangle_other3.1393.6544002
X-RAY DIFFRACTIONr_scbond_it3.1332.7062966
X-RAY DIFFRACTIONr_scbond_other3.1322.7062967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5873.9384469
X-RAY DIFFRACTIONr_long_range_B_refined6.11329.4836759
X-RAY DIFFRACTIONr_long_range_B_other5.96328.9516579
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A79280.06
12B79280.06
21A78980.08
22C78980.08
31B78270.09
32C78270.09
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 342 -
Rwork0.227 6451 -
obs--100 %

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