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- PDB-4tx3: Complex of the X-domain and OxyB from Teicoplanin Biosynthesis -

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Basic information

Entry
Database: PDB / ID: 4tx3
TitleComplex of the X-domain and OxyB from Teicoplanin Biosynthesis
Components
  • OxyB protein
  • Peptide synthetase, module 7
KeywordsOXIDOREDUCTASE / non-ribosomal peptide synthetase / condensation-type domain / teicoplanin biosynthesis / oxygenase complex / hydrolase
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / glycosyltransferase activity / catalytic activity / phosphopantetheine binding / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / monooxygenase activity / iron ion binding / heme binding / cytosol
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site ...Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Thioesterase / Thioesterase domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / AMP-dependent synthetase/ligase / AMP-binding enzyme / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-binding enzyme, C-terminal domain superfamily / Cytochrome P450, B-class / Cytochrome p450 / Cytochrome P450 / Cytochrome P450, conserved site / Cytochrome P450 cysteine heme-iron ligand signature. / Cytochrome P450 / Cytochrome P450 superfamily / Cytochrome P450 / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Peptide synthetase, module 7 / Oxidation protein CepF/oxidation protein CepG
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPeschke, M. / Haslinger, K. / Cryle, M.J.
CitationJournal: Nature / Year: 2015
Title: X-domain of peptide synthetases recruits oxygenases crucial for glycopeptide biosynthesis.
Authors: Haslinger, K. / Peschke, M. / Brieke, C. / Maximowitsch, E. / Cryle, M.J.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OxyB protein
B: Peptide synthetase, module 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9948
Polymers97,9312
Non-polymers1,0636
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-72 kcal/mol
Surface area36510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.340, 94.010, 125.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein OxyB protein


Mass: 44494.746 Da / Num. of mol.: 1 / Fragment: UNP residues 1-398
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: tcp20 / Plasmid: pET24d / Details (production host): GB1-fusion protein / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AY8, unspecific monooxygenase
#2: Protein Peptide synthetase, module 7


Mass: 53435.977 Da / Num. of mol.: 1 / Fragment: UNP residues 1047-1511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Actinoplanes teichomyceticus (bacteria)
Gene: teiD / Plasmid: pET151d / Details (production host): TOPO plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6ZZJ3

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Non-polymers , 4 types, 259 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.63 Å3/Da / Density % sol: 53.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 100 mM Bis-Tris, 200 mM (NH4)2SO4, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.978 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 36333 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 40.38 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.093 / Χ2: 0.973 / Net I/σ(I): 14.96 / Num. measured all: 212554
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.70.9050.4493.8343514735873510.49299.9
2.7-2.90.9660.2745.9833265552655210.29999.9
2.9-3.10.9810.1858.4923948416741640.20399.9
3.1-40.9960.08317.495979710161101550.09199.9
4-60.9980.04928.2136650633563320.054100
6-80.9980.04628.859110159515940.0599.9
8-100.9990.03536.2330875725690.03999.5
10-200.9980.03637.5727945625600.0499.6
200.9980.03736.0338994870.0492.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TX2, 4TVF

4tx2

4tvf


Resolution: 2.5→47.005 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 1817 5 %Random selection
Rwork0.1682 34513 --
obs0.1711 36330 99.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 113.42 Å2 / Biso mean: 43.5361 Å2 / Biso min: 21.45 Å2
Refinement stepCycle: final / Resolution: 2.5→47.005 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6466 0 67 253 6786
Biso mean--45.7 41.22 -
Num. residues----830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086659
X-RAY DIFFRACTIONf_angle_d1.1819069
X-RAY DIFFRACTIONf_chiral_restr0.041021
X-RAY DIFFRACTIONf_plane_restr0.0051207
X-RAY DIFFRACTIONf_dihedral_angle_d15.3022493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5-2.56760.27951380.213926222760
2.5676-2.64320.29131360.2125942730
2.6432-2.72850.33811390.215226252764
2.7285-2.8260.28091370.205626172754
2.826-2.93910.28071390.203726262765
2.9391-3.07280.28991380.191726292767
3.0728-3.23480.27171390.192226352774
3.2348-3.43740.25851380.180926272765
3.4374-3.70270.211390.173426462785
3.7027-4.07520.22771410.153926762817
4.0752-4.66440.18161410.135526712812
4.6644-5.87480.2081430.145927212864
5.8748-47.01330.15991490.146928242973

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