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- PDB-5hyh: CmlI (chemically reduced state), arylamine oxygenase of chloramph... -

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Basic information

Entry
Database: PDB / ID: 5hyh
TitleCmlI (chemically reduced 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
: / 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 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 23, 2022Group: Author supporting evidence / Database references / Derived calculations
Category: database_2 / pdbx_audit_support / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Revision 1.5Sep 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)36,4244
Polymers36,1631
Non-polymers2623
Water2,144119
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8498
Polymers72,3252
Non-polymers5246
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_677x-y+1,-y+2,-z+7/31
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.961, 56.961, 151.099
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-607-

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 (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: isolated from a natural source / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: Hexagonal
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, L-(+)-ammonium tartrate dibasic / 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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 11, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 19182 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 38
Reflection shellResolution: 2.03→2.07 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.374 / Mean I/σ(I) obs: 5.4 / % possible all: 99.9

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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→29.99 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.382 / SU ML: 0.122 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23877 1496 7.8 %RANDOM
Rwork0.18929 ---
obs0.19308 17615 99.32 %-
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: 37.128 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.03→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2294 0 12 119 2425
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192387
X-RAY DIFFRACTIONr_bond_other_d0.0010.022235
X-RAY DIFFRACTIONr_angle_refined_deg1.231.9363244
X-RAY DIFFRACTIONr_angle_other_deg0.80235111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0265291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.27123.306124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.65715392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6611524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022742
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02586
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: 2.025→2.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 91 -
Rwork0.219 1222 -
obs--95.84 %

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