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- PDB-2og7: Cystal structure of asparagine oxygenase in complex with Fe(II), ... -

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Basic information

Entry
Database: PDB / ID: 2og7
TitleCystal structure of asparagine oxygenase in complex with Fe(II), 2S,3S-3-hydroxyasparagine and succinate
Componentsasparagine oxygenase
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT / nonribosomal peptide synthesis / non-heme iron(II) / alpha-ketoglutarate oxygenase / beta-hydroxylated amino acid
Function / homology
Function and homology information


L-asparagine hydroxylase / antibiotic biosynthetic process / oxidoreductase activity / iron ion binding
Similarity search - Function
: / Clavaminate synthase-like / Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-HYDROXYASPARAGINE / : / SUCCINIC ACID / L-asparagine oxygenase
Similarity search - Component
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsEssen, L.-O. / Strieker, M.
CitationJournal: Acs Chem.Biol. / Year: 2007
Title: Mechanistic and structural basis of stereospecific Cbeta-hydroxylation in calcium-dependent antibiotic, a daptomycin-type lipopeptide
Authors: Strieker, M. / Kopp, F. / Mahlert, C. / Essen, L.-O. / Marahiel, M.A.
History
DepositionJan 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: asparagine oxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2724
Polymers38,9501
Non-polymers3223
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.308, 91.308, 90.867
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-7218-

HOH

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Components

#1: Protein asparagine oxygenase / Putative oxygenase


Mass: 38949.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Species: Streptomyces coelicolor / Strain: DSMZ 40783
Description: expression plasmid encodes for N-terminal His-7-tag for IMAC
Gene: sco3236 (asnO) / Plasmid: pQTEVMS01 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Z4Z5
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-AHB / BETA-HYDROXYASPARAGINE


Type: L-peptide linking / Mass: 148.117 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8N2O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.81 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 2.5 M sodium acetate, 0.1 M Hepes, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.808 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.808 Å / Relative weight: 1
ReflectionResolution: 1.65→23 Å / Num. obs: 51815 / % possible obs: 99.4 % / Observed criterion σ(F): 191425 / Redundancy: 3.69 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.1
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.49 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 1.7 / Num. unique all: 7385 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCD 165data collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1DRY

1dry


Resolution: 1.66→22.91 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.518 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.074 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1582 3.1 %RANDOM
Rwork0.168 ---
all0.18371 ---
obs0.1681 51776 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20.27 Å20 Å2
2--0.54 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.66→22.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 19 258 2725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212522
X-RAY DIFFRACTIONr_bond_other_d0.0020.021723
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9753444
X-RAY DIFFRACTIONr_angle_other_deg0.87134154
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5575318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.1422.458118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3715375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8641531
X-RAY DIFFRACTIONr_chiral_restr0.0610.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022866
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02529
X-RAY DIFFRACTIONr_nbd_refined0.2110.2512
X-RAY DIFFRACTIONr_nbd_other0.2080.21926
X-RAY DIFFRACTIONr_nbtor_refined0.170.21235
X-RAY DIFFRACTIONr_nbtor_other0.0830.21376
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2176
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1290.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3380.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.226
X-RAY DIFFRACTIONr_mcbond_it0.7751.52048
X-RAY DIFFRACTIONr_mcbond_other0.1271.5636
X-RAY DIFFRACTIONr_mcangle_it0.84522572
X-RAY DIFFRACTIONr_scbond_it1.57431041
X-RAY DIFFRACTIONr_scangle_it2.4084.5872
LS refinement shellResolution: 1.66→1.702 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 95 -
Rwork0.26 3535 -
obs-3630 96.98 %
Refinement TLS params.Method: refined / Origin x: -5.2883 Å / Origin y: 62.4197 Å / Origin z: -12.455 Å
111213212223313233
T-0.0633 Å2-0.0248 Å2-0.0113 Å2--0.046 Å2-0.0063 Å2---0.0881 Å2
L0.2002 °20.1254 °2-0.0722 °2-2.916 °2-0.3454 °2--0.5093 °2
S0.1249 Å °-0.0433 Å °-0.0017 Å °0.0701 Å °-0.2363 Å °0.0101 Å °0.0521 Å °-0.0208 Å °0.1113 Å °
Refinement TLS groupSelection: ALL

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