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- PDB-5hyg: CmlI (peroxo bound state), arylamine oxygenase of chloramphenicol... -

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Basic information

Entry
Database: PDB / ID: 5hyg
TitleCmlI (peroxo bound state), arylamine oxygenase of chloramphenicol biosynthetic pathway
ComponentsUncharacterized protein
KeywordsMETAL BINDING PROTEIN / Oxygen activation / Non-heme iron / Diiron cluster / Antibiotic biosynthesis
Function / homology
Function and homology information


alpha-N-dichloroacetyl-p-aminophenylserinol N-oxygenase / antibiotic biosynthetic process / oxidoreductase activity / metal ion binding
Similarity search - Function
P-aminobenzoate N-oxygenase AurF / P-aminobenzoate N-oxygenase AurF / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / HYDROGEN PEROXIDE / L(+)-TARTARIC ACID / Alpha-N-dichloroacetyl-p-aminophenylserinol N-oxygenase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsKnoot, C.J. / Lipscomb, J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM100943 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM118030 United States
CitationJournal: J.Biol.Inorg.Chem. / Year: 2016
Title: Crystal structure of CmlI, the arylamine oxygenase from the chloramphenicol biosynthetic pathway.
Authors: Knoot, C.J. / Kovaleva, E.G. / Lipscomb, J.D.
History
DepositionFeb 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2016Group: Database references
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support ...database_2 / pdbx_audit_support / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4585
Polymers36,1631
Non-polymers2964
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.539, 56.539, 150.474
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-571-

HOH

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Components

#1: Protein Uncharacterized protein


Mass: 36162.516 Da / Num. of mol.: 1 / Fragment: residues 33-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_0924 / Plasmid: pVP91A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2RB83
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 1.9 Å3/Da / Density % sol: 35 % / Description: Triangular
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 1500, L-(+)-ammonium tartrate / PH range: 6.5-6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 27, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 15532 / % possible obs: 88.4 % / Redundancy: 5.5 % / Biso Wilson estimate: 29.3 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 29
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.408 / Mean I/σ(I) obs: 6.9 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERv2.5.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CHH

3chh


Resolution: 2.03→22 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.657 / SU ML: 0.129 / Cross valid method: THROUGHOUT / ESU R: 0.287 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25114 1246 8 %RANDOM
Rwork0.18521 ---
obs0.19038 14278 82.89 %-
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: 39.529 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.03→22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 14 74 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192334
X-RAY DIFFRACTIONr_bond_other_d0.0010.022179
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9323171
X-RAY DIFFRACTIONr_angle_other_deg0.81434981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.025284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60423.223121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03315379
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6471523
X-RAY DIFFRACTIONr_chiral_restr0.0790.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022681
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02578
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 2.032→2.084 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 96 -
Rwork0.22 1095 -
obs--87.06 %

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