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- PDB-8w2d: holo-PCP-Thioesterase di-domain structure from the sulfazecin bio... -

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Basic information

Entry
Database: PDB / ID: 8w2d
Titleholo-PCP-Thioesterase di-domain structure from the sulfazecin biosynthetic nonribosomal peptide synthetase, SulM
ComponentsNon-ribosomal peptide synthetase
KeywordsHYDROLASE / Thioesterase domain / NRPS / PCP domain / nonribosomal peptide synthetase / Sulfazecin
Function / homology
Function and homology information


biosynthetic process / phosphopantetheine binding / catalytic activity
Similarity search - Function
Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / PKS_PP_betabranch / 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. ...Non-ribosomal peptide synthase / Condensation domain / Condensation domain / Amino acid adenylation domain / PKS_PP_betabranch / 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 / AMP-binding enzyme, C-terminal domain superfamily / 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
4'-PHOSPHOPANTETHEINE / Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesParaburkholderia acidicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsPatel, K.D. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM136235 United States
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The structure of the monobactam-producing thioesterase domain of SulM forms a unique complex with the upstream carrier protein domain.
Authors: Patel, K.D. / Oliver, R.A. / Lichstrahl, M.S. / Li, R. / Townsend, C.A. / Gulick, A.M.
History
DepositionFeb 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Non-ribosomal peptide synthetase
B: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,8669
Polymers74,8392
Non-polymers1,0277
Water50428
1
A: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9645
Polymers37,4191
Non-polymers5454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9024
Polymers37,4191
Non-polymers4823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.116, 79.072, 70.484
Angle α, β, γ (deg.)90.000, 93.515, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

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
11METMETLEULEU(chain 'A' and ((resid 2659 through 2660 and (name N...AA2659 - 272020 - 81
12SERSERCYSCYS(chain 'A' and ((resid 2659 through 2660 and (name N...AA2727 - 297988 - 340
13PNSPNSPNSPNS(chain 'A' and ((resid 2659 through 2660 and (name N...AC3001
21METMETLEULEU(chain 'B' and ((resid 2659 through 2660 and (name N...BB2659 - 272020 - 81
22SERSERCYSCYS(chain 'B' and ((resid 2659 through 2660 and (name N...BB2727 - 297988 - 340
23PNSPNSPNSPNS(chain 'B' and ((resid 2659 through 2660 and (name N...BG3001

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Components

#1: Protein Non-ribosomal peptide synthetase / SulM


Mass: 37419.293 Da / Num. of mol.: 2 / Fragment: Thioesterase didomain
Source method: isolated from a genetically manipulated source
Details: The protein was expressed and crystallized with His-tag from expression vector.
Source: (gene. exp.) Paraburkholderia acidicola (bacteria) / Strain: ATCC 31363 / Gene: sulM, BWP39_23695 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1I9RH13
#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.95 % / Description: Thin rods
Crystal growTemperature: 293 K / Method: microbatch / Details: 1.8M tribasic ammonium citrate / PH range: 7.0-7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→47.8 Å / Num. obs: 17876 / % possible obs: 97.7 % / Redundancy: 4 % / Biso Wilson estimate: 50.47 Å2 / CC1/2: 0.99 / Net I/σ(I): 8.1
Reflection shellResolution: 2.7→2.84 Å / Num. unique obs: 2516 / CC1/2: 0.65 / % possible all: 94.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHASERphasing
autoPROC1.05data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→40.47 Å / SU ML: 0.3825 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.3671 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2569 1768 9.94 %
Rwork0.2208 16018 -
obs0.2244 17786 97.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.96 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4766 0 62 28 4856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00354924
X-RAY DIFFRACTIONf_angle_d0.80146703
X-RAY DIFFRACTIONf_chiral_restr0.0468772
X-RAY DIFFRACTIONf_plane_restr0.0044871
X-RAY DIFFRACTIONf_dihedral_angle_d9.76482899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.33741110.28551090X-RAY DIFFRACTION86.65
2.77-2.850.31451420.29121259X-RAY DIFFRACTION98.87
2.85-2.940.371340.30621235X-RAY DIFFRACTION97.79
2.94-3.050.34121320.27131223X-RAY DIFFRACTION97.76
3.05-3.170.30881380.25051250X-RAY DIFFRACTION98.86
3.17-3.310.26491470.23071266X-RAY DIFFRACTION99.51
3.31-3.490.27461340.24571227X-RAY DIFFRACTION98.41
3.49-3.710.26611330.23711211X-RAY DIFFRACTION96.07
3.71-3.990.2691400.2121252X-RAY DIFFRACTION98.03
3.99-4.40.2221390.17881247X-RAY DIFFRACTION98.58
4.4-5.030.19971380.18441236X-RAY DIFFRACTION96.49
5.03-6.330.25991400.21221253X-RAY DIFFRACTION99
6.33-40.470.21081400.19961269X-RAY DIFFRACTION96.77

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