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- PDB-7crn: The Functional Characterization and Crystal Structure of the Bifu... -

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Basic information

Entry
Database: PDB / ID: 7crn
TitleThe Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization
ComponentsNon-ribosomal peptide synthetase 4
KeywordsBIOSYNTHETIC PROTEIN / hydrolase fold / thioesterase / epimerization / cyclization
Function / homology
Function and homology information


amide biosynthetic process / polyketide biosynthetic process / : / organonitrogen compound biosynthetic process / carboxylic acid metabolic process / lipid biosynthetic process / phosphopantetheine binding / antibiotic biosynthetic process / catalytic activity
Similarity search - Function
Non-ribosomal peptide synthase / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain ...Non-ribosomal peptide synthase / Polyketide synthase, thioesterase domain / Thioesterase / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation 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 / Phosphopantetheine attachment site. / 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 4
Similarity search - Component
Biological speciesStreptomyces abietis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsYu, J.H. / Song, J. / Chi, C.B. / Ma, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21877002, 81673332, 81991525, 81573326 China
CitationJournal: Acs Catalysis / Year: 2021
Title: Functional Characterization and Crystal Structure of the Bifunctional Thioesterase Catalyzing Epimerization and Cyclization in Skyllamycin Biosynthesis
Authors: Yu, J. / Juan, S. / Chi, C. / Liu, T. / Geng, T. / Cai, Z. / Dong, W. / Shi, C. / Ma, X. / Zhang, Z. / Ma, X. / Xing, B. / Jin, H. / Zhang, L. / Dong, S. / Yang, D. / Ma, M.
History
DepositionAug 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-ribosomal peptide synthetase 4
B: Non-ribosomal peptide synthetase 4
C: Non-ribosomal peptide synthetase 4


Theoretical massNumber of molelcules
Total (without water)90,6633
Polymers90,6633
Non-polymers00
Water1,65792
1
A: Non-ribosomal peptide synthetase 4
C: Non-ribosomal peptide synthetase 4


Theoretical massNumber of molelcules
Total (without water)60,4422
Polymers60,4422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-10 kcal/mol
Surface area20950 Å2
MethodPISA
2
B: Non-ribosomal peptide synthetase 4

B: Non-ribosomal peptide synthetase 4


Theoretical massNumber of molelcules
Total (without water)60,4422
Polymers60,4422
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area1850 Å2
ΔGint-9 kcal/mol
Surface area20900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.132, 117.665, 209.793
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 8 through 157 or resid 163 through 275))
21(chain B and (resid 8 through 157 or resid 163 through 275))
31chain C

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLYGLYASPASP(chain A and (resid 8 through 157 or resid 163 through 275))AA8 - 1578 - 157
12PROPROGLYGLY(chain A and (resid 8 through 157 or resid 163 through 275))AA163 - 275163 - 275
21GLYGLYASPASP(chain B and (resid 8 through 157 or resid 163 through 275))BB8 - 1578 - 157
22PROPROGLYGLY(chain B and (resid 8 through 157 or resid 163 through 275))BB163 - 275163 - 275
31GLYGLYGLYGLYchain CCC8 - 2758 - 275

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Components

#1: Protein Non-ribosomal peptide synthetase 4 / Skyxy-TE


Mass: 30220.977 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces abietis (bacteria) / Gene: nrps4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1J0R317
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe Ala206 in the sequence is different naturally to the published homologues (A0A1J0R317). ...The Ala206 in the sequence is different naturally to the published homologues (A0A1J0R317). Sequence used in this study was derived from Streptomyces strain isolated from a marine coral sample, which has not been deposited to any database at the time of data annotation.

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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: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 60% Tacsimate, pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.257→34.97 Å / Num. obs: 38795 / % possible obs: 98.7 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 42.8
Reflection shellResolution: 2.257→2.33 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 1873

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
Cootmodel building
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TEJ

3tej


Resolution: 2.26→34.97 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2061 1966 5.13 %RANDOM
Rwork0.1776 36384 --
obs0.1792 38350 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.32 Å2 / Biso mean: 45.1036 Å2 / Biso min: 18.15 Å2
Refinement stepCycle: final / Resolution: 2.26→34.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6057 0 0 92 6149
Biso mean---41.55 -
Num. residues----791
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2394X-RAY DIFFRACTION10.153TORSIONAL
12B2394X-RAY DIFFRACTION10.153TORSIONAL
13C2394X-RAY DIFFRACTION10.153TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.26-2.310.32511010.24151872197370
2.31-2.380.32641420.216826682810100
2.38-2.450.20711470.205826952842100
2.45-2.520.28961460.208426862832100
2.52-2.610.28931480.20822682283099
2.61-2.720.23191430.21482659280299
2.72-2.840.28061450.21582588273396
2.84-2.990.22821450.21092631277699
2.99-3.180.23581400.22663280398
3.18-3.430.22781370.18512648278597
3.43-3.770.23611360.16262600273695
3.77-4.310.16031440.14542578272294
4.31-5.430.15551420.14712658280096
5.43-34.970.16271500.17022756290695

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