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- PDB-4tx2: Crystal structure of the X-domain from teicoplanin biosynthesis -

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Basic information

Entry
Database: PDB / ID: 4tx2
TitleCrystal structure of the X-domain from teicoplanin biosynthesis
ComponentsNon-ribosomal peptide synthetase
KeywordsPROTEIN BINDING / non-ribosomal peptide synthetase / condensation type domain / teicoplanin biosynthesis / oxygenase complex
Function / homology
Function and homology information


amide biosynthetic process / : / organonitrogen compound biosynthetic process / secondary metabolite biosynthetic process / lipid biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Chloramphenicol acetyltransferase-like domain superfamily / Putative AMP-binding domain signature. / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesActinoplanes teichomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsPeschke, M. / Haslinger, K. / Cryle, M.J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationEmmy-Noether Program, CR 392/1-1 Germany
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 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1Dec 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
B: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)53,4361
Polymers53,4361
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area20300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.990, 134.990, 54.370
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Non-ribosomal peptide synthetase


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: tcp12 / Plasmid: pET24d / Details (production host): GB1 fusion protein / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q70AZ6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.68 Å3/Da / Density % sol: 54.04 %
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: 0.9797 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 2.9→48 Å / Num. obs: 12768 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 20.5 % / Biso Wilson estimate: 42.4 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.122 / Χ2: 0.914 / Net I/σ(I): 24.31 / Num. measured all: 261201
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.9-3.20.9830.3629.0967705322932270.37199.9
3.2-3.40.9930.21914.3231216157715760.22599.9
3.4-3.60.9960.16119.1624645121112110.166100
3.6-3.70.9970.14122.5115405395390.145100
3.7-3.80.9980.12225.0196674634630.125100
3.8-3.90.9980.11126.7288934264260.114100
3.9-40.9980.10928.2881383853850.111100
4-4.10.9980.09330.6371383463460.096100
4.1-4.20.9990.09132.364003183170.09499.7
4.2-4.30.9980.09331.8856652832830.096100
4.3-4.50.9990.0835.4298425035030.082100
4.5-50.9990.07538.12193049339330.077100
5-60.9990.08533.8321858105610560.087100
6-80.9990.07736.33167528558550.079100
8-1010.04657.1761643053050.047100
10-200.9990.04162.5654812992990.042100
2010.03570.7779349440.03689.8

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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: 2JGP

2jgp


Resolution: 2.9→44.186 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 25.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 639 5.01 %Random Selection
Rwork0.1922 12115 --
obs0.1951 12754 99.97 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 103.88 Å2 / Biso mean: 30.6939 Å2 / Biso min: 3.42 Å2
Refinement stepCycle: final / Resolution: 2.9→44.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3519 0 0 18 3537
Biso mean---24.85 -
Num. residues----452
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023587
X-RAY DIFFRACTIONf_angle_d0.5924885
X-RAY DIFFRACTIONf_chiral_restr0.022559
X-RAY DIFFRACTIONf_plane_restr0.003656
X-RAY DIFFRACTIONf_dihedral_angle_d12.1141338
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.9001-3.1240.3481260.258923852511
3.124-3.43820.28571260.231824062532
3.4382-3.93550.26341280.199124262554
3.9355-4.95730.22541270.158224082535
4.9573-44.1910.20651320.17224902622

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