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- PDB-3i3l: Crystal structure of CmlS, a flavin-dependent halogenase -

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Basic information

Entry
Database: PDB / ID: 3i3l
TitleCrystal structure of CmlS, a flavin-dependent halogenase
ComponentsAlkylhalidase CmlS
KeywordsHYDROLASE / CmlS / flavin-dependent halogenase / chloramphenicol biosynthesis / halogenation reaction / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


FAD binding / oxidoreductase activity
Similarity search - Function
Enolase-like; domain 1 - #160 / : / Chloramphenicol halogenase CmlS C-terminal domain / Tryptophan halogenase / : / FAD-binding domain / FAD binding domain / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Enolase-like; domain 1 - #160 / : / Chloramphenicol halogenase CmlS C-terminal domain / Tryptophan halogenase / : / FAD-binding domain / FAD binding domain / Enolase-like; domain 1 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Alkylhalidase CmlS
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsPodzelinska, K. / Soares, A. / Jia, Z. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Chloramphenicol Biosynthesis: The Structure of CmlS, a Flavin-Dependent Halogenase Showing a Covalent Flavin-Aspartate Bond
Authors: Podzelinska, K. / Latimer, R. / Bhattacharya, A. / Vining, L.C. / Zechel, D.L. / Jia, Z.
History
DepositionJun 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Alkylhalidase CmlS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3202
Polymers66,5341
Non-polymers7861
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)208.090, 57.736, 59.883
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alkylhalidase CmlS


Mass: 66534.414 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (bacteria) / Gene: cmlS / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9AL91
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAUTHORS STATE THAT THE CMLS SEQUENCE DEPOSITED IN DATABASE IS INCORRECT AND THE NATURALLY OCCURING ...AUTHORS STATE THAT THE CMLS SEQUENCE DEPOSITED IN DATABASE IS INCORRECT AND THE NATURALLY OCCURING PROTEIN DOES NOT ACTUALLY HAVE THESE RESIDUES. SO RESIDUES ILE 303 - VAL 308 ARE NOT PRESENT IN THE CRYSTAL

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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: 2.68 Å3/Da / Density % sol: 54.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 0.1 M Na HEPES, 19% PEG 3350, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 2, 2008
Details: vertically collimating mirror, doubly focusing toroidal mirror
RadiationMonochromator: channel-cut Si(111) crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 37463 / Num. obs: 36054 / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.2 % / Rsym value: 0.077 / Net I/σ(I): 35.7
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.1 / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.5.0066refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.981 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUES F390, F408, R409, D499, R559, L560 WERE REFINED AS GLYCINE, AND RESIDUE R481 AS ALANINE, BECAUSE THE SIDE CHAIN DENSITY WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE RESIDUES F390, F408, R409, D499, R559, L560 WERE REFINED AS GLYCINE, AND RESIDUE R481 AS ALANINE, BECAUSE THE SIDE CHAIN DENSITY WAS NOT OBSERVED FOR THESE RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.26056 1786 5 %RANDOM
Rwork0.20031 ---
obs0.20329 34078 99.43 %-
all-34273 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.22 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-0.03 Å2
2---1.74 Å20 Å2
3---2.17 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4356 0 53 232 4641
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0224514
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9546113
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.935547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94623.17224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.5415734
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6311540
X-RAY DIFFRACTIONr_chiral_restr0.1240.2643
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213487
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.3251.52715
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.29124342
X-RAY DIFFRACTIONr_scbond_it3.44331799
X-RAY DIFFRACTIONr_scangle_it5.0584.51771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 115 -
Rwork0.234 2385 -
obs--94.8 %

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