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- PDB-2q6i: salL with ClDA and LMet -

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Basic information

Entry
Database: PDB / ID: 2q6i
TitlesalL with ClDA and LMet
ComponentsHypothetical protein
KeywordsBIOSYNTHETIC PROTEIN / chlorinase / ClDA and L-Met 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
5'-CHLORO-5'-DEOXYADENOSINE / METHIONINE / DI(HYDROXYETHYL)ETHER / Adenosyl-chloride synthase
Similarity search - Component
Biological speciesSalinispora tropica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9296
Polymers30,1751
Non-polymers7535
Water93752
1
A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules

A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,78618
Polymers90,5263
Non-polymers2,26015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area11830 Å2
ΔGint-39 kcal/mol
Surface area29260 Å2
MethodPISA, PQS
2
A: Hypothetical protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)185,57136
Polymers181,0526
Non-polymers4,52030
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_655-x+y+1,y,-z+1/21
crystal symmetry operation12_545x,x-y-1,-z+1/21
Buried area27340 Å2
ΔGint-103 kcal/mol
Surface area54840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.030, 111.030, 93.310
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-618-

HOH

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Components

#1: Protein Hypothetical protein


Mass: 30175.256 Da / Num. of mol.: 1
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-5CD / 5'-CHLORO-5'-DEOXYADENOSINE


Mass: 285.687 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12ClN5O3
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2.75 Å3/Da / Density % sol: 55.26 %
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: Nov 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: 2.6→20 Å / Num. obs: 10922 / Redundancy: 14.92 % / Rsym value: 0.153 / Net I/σ(I): 19.39
Reflection shellResolution: 2.6→2.76 Å / Redundancy: 14.65 % / Rsym value: 0.454

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RQP

1rqp


Resolution: 2.6→19.94 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.868 / SU B: 9.457 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26203 521 4.8 %RANDOM
Rwork0.20612 ---
obs0.20879 10353 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.261 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1999 0 49 52 2100
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222132
X-RAY DIFFRACTIONr_angle_refined_deg1.2261.9892915
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.38624.41986
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.46315298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5761510
X-RAY DIFFRACTIONr_chiral_restr0.0820.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021628
X-RAY DIFFRACTIONr_nbd_refined0.1910.2899
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.211
X-RAY DIFFRACTIONr_mcbond_it0.4951.51385
X-RAY DIFFRACTIONr_mcangle_it0.89922196
X-RAY DIFFRACTIONr_scbond_it1.1593835
X-RAY DIFFRACTIONr_scangle_it1.8994.5719
LS refinement shellResolution: 2.601→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 --
Rwork0.228 728 -
all-37 -
obs--99.74 %

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