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- PDB-2q6o: SalL-Y70T with SAM and Cl -

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Basic information

Entry
Database: PDB / ID: 2q6o
TitleSalL-Y70T with SAM and Cl
ComponentsHypothetical Protein
KeywordsBIOSYNTHETIC PROTEIN / chlorinase / Y70T mutant SAM and Cl complex
Function / homology
Function and homology information


adenosyl-chloride synthase / transferase activity, transferring alkyl or aryl (other than methyl) groups
Similarity search - Function
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 ...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
S-ADENOSYLMETHIONINE / Adenosyl-chloride synthase
Similarity search - Component
Biological speciesSalinispora tropica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / 2Q6I / Resolution: 2 Å
AuthorsNoel, J.P. / Pojer, F.
CitationJournal: Nat.Chem.Biol. / Year: 2008
Title: Discovery and characterization of a marine bacterial SAM-dependent chlorinase
Authors: Eustaquio, A.S. / Pojer, F. / Noel, J.P. / Moore, B.S.
History
DepositionJun 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical Protein
B: Hypothetical Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0946
Polymers60,2262
Non-polymers8684
Water2,108117
1
A: Hypothetical Protein
hetero molecules

A: Hypothetical Protein
hetero molecules

A: Hypothetical Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6419
Polymers90,3403
Non-polymers1,3026
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8300 Å2
ΔGint-71 kcal/mol
Surface area30110 Å2
MethodPISA, PQS
2
B: Hypothetical Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5473
Polymers30,1131
Non-polymers4342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Hypothetical Protein
hetero molecules

B: Hypothetical Protein
hetero molecules

B: Hypothetical Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,6419
Polymers90,3403
Non-polymers1,3026
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-y+2,x-y+2,z1
crystal symmetry operation3_575-x+y,-x+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.530, 111.530, 47.610
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3

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Components

#1: Protein Hypothetical Protein


Mass: 30113.186 Da / Num. of mol.: 2 / Mutation: Y70T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salinispora tropica (bacteria) / Strain: CNB-440 / Gene: salL / Plasmid: pHIs8 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A4X3Q0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE


Mass: 398.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H22N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.85 Å3/Da / Density % sol: 56.91 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 28% PEG3350, 0.3M KCL, 2mM DTT, 0.1 M MOPSO, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 1, 2006
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 44611 / Redundancy: 3.5 % / Rmerge(I) obs: 0.156 / Net I/σ(I): 7.13
Reflection shellResolution: 2→2.12 Å / Redundancy: 3.34 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 4.36

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CNS1.1refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: 2Q6I / Resolution: 2→19.27 Å / Cor.coef. Fo:Fc: 0.813 / Cor.coef. Fo:Fc free: 0.752 / SU B: 5.711 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.31298 2253 5 %RANDOM
Rwork0.26629 ---
obs0.26869 42427 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.274 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2→19.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4030 0 56 117 4203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224182
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0431.9845730
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.95536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12924.524168
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.38515598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6511520
X-RAY DIFFRACTIONr_chiral_restr0.1530.2674
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023184
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.230.21844
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3190.22773
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2186
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.291
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0841.52779
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63124352
X-RAY DIFFRACTIONr_scbond_it2.67831616
X-RAY DIFFRACTIONr_scangle_it3.7934.51378
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 166 -
Rwork0.255 3145 -
obs--99.94 %

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