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- PDB-6ta8: Crystal structure of the epimerization domain from the third modu... -

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Basic information

Entry
Database: PDB / ID: 6ta8
TitleCrystal structure of the epimerization domain from the third module of tyrocidine synthetase B, TycB3(E)
ComponentsTyrocidine synthase 2
KeywordsBIOSYNTHETIC PROTEIN / NRPS / epimerization domain / epimerisation domain / chloramphenicol acetyltransferase / epimerase / isomerase
Function / homology
Function and homology information


phenylalanine racemase (ATP-hydrolysing) / phenylalanine racemase (ATP-hydrolyzing) activity / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / ATP binding
Similarity search - Function
Non-ribosomal peptide synthase / 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 / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily ...Non-ribosomal peptide synthase / 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 / Putative AMP-binding domain signature. / Chloramphenicol acetyltransferase-like domain superfamily / Polyketide synthase, phosphopantetheine-binding domain / Phosphopantetheine attachment site / AMP-dependent synthetase/ligase / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain
Similarity search - Domain/homology
Tyrocidine synthase 2
Similarity search - Component
Biological speciesBrevibacillus parabrevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFage, C.D. / Marahiel, M.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation Germany
LOEWE Center for Synthetic Microbiology Germany
CitationJournal: Acs Catalysis / Year: 2021
Title: Communication Breakdown: Dissecting the COM Interfaces between the Subunits of Nonribosomal Peptide Synthetases
Authors: Fage, C.D. / Kosol, S. / Jenner, M. / Oster, C. / Gallo, A. / Kaniusaite, M. / Steinbach, R. / Staniforth, M. / Stavros, V.G. / Marahiel, M.A. / Cryle, M.J. / Lewandowski, J.R.
History
DepositionOct 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
SupersessionJun 2, 2021ID: 5M6P
Revision 1.1Jun 2, 2021Group: Advisory / Category: pdbx_database_PDB_obs_spr
Revision 1.2Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Jan 24, 2024Group: 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: Tyrocidine synthase 2
B: Tyrocidine synthase 2


Theoretical massNumber of molelcules
Total (without water)113,7212
Polymers113,7212
Non-polymers00
Water4,035224
1
A: Tyrocidine synthase 2


Theoretical massNumber of molelcules
Total (without water)56,8611
Polymers56,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrocidine synthase 2


Theoretical massNumber of molelcules
Total (without water)56,8611
Polymers56,8611
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.661, 120.661, 256.002
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x+1/3,y+2/3,z+2/3
#5: -y+1/3,x-y+2/3,z+2/3
#6: -x+y+1/3,-x+2/3,z+2/3
#7: x+2/3,y+1/3,z+1/3
#8: -y+2/3,x-y+1/3,z+1/3
#9: -x+y+2/3,-x+1/3,z+1/3

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Components

#1: Protein Tyrocidine synthase 2 / Tyrocidine synthase II


Mass: 56860.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Residues N3113-I3587 of TycB / Source: (gene. exp.) Brevibacillus parabrevis (bacteria) / Gene: tycB / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O30408, phenylalanine racemase (ATP-hydrolysing)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 3.52 Å3/Da / Density % sol: 65.07 % / Description: Plate-like
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M magnesium nitrate, 20% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.4→49.262 Å / Num. obs: 54344 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 48.9 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.074 / Rrim(I) all: 0.166 / Net I/σ(I): 8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.4-2.474.81.4562170045030.460.7411.637199.9
10.18-49.2650.04635247060.9970.0220.05127.399.1

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Processing

Software
NameVersionClassification
PHENIX1.13-2998refinement
PHENIX1.10.1-2155phasing
XDSJan 26, 2018data reduction
Aimless0.7.4data scaling
Coot0.8.9.2model building
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PHYRE2 model of 5ISX (residues 522-1071)

5isx


Resolution: 2.4→49.262 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 32.03
RfactorNum. reflection% reflection
Rfree0.2759 2803 5.16 %
Rwork0.2447 --
obs0.2463 54324 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 113.55 Å2 / Biso mean: 55.9472 Å2 / Biso min: 22.13 Å2
Refinement stepCycle: final / Resolution: 2.4→49.262 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7189 0 563 226 7978
Biso mean--58.02 52.48 -
Num. residues----815
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.4-2.44140.38561410.35212611
2.4414-2.48580.37321540.34732535
2.4858-2.53360.40521270.32392571
2.5336-2.58530.34991180.32112570
2.5853-2.64150.32981390.30962615
2.6415-2.7030.3761420.31592582
2.703-2.77060.35221560.30942563
2.7706-2.84550.35091480.30782535
2.8455-2.92920.351210.30192606
2.9292-3.02370.31871460.29442587
3.0237-3.13180.29711290.28132588
3.1318-3.25720.29831810.27672551
3.2572-3.40540.29651170.24492548
3.4054-3.58480.27831520.23372600
3.5848-3.80940.26651510.22282561
3.8094-4.10340.25551440.21752561
4.1034-4.5160.19221270.20162592
4.516-5.16890.23061350.20282580
5.1689-6.50990.26741370.23752581
6.5099-49.2620.24471380.21552584

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