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- PDB-8w2c: Thioesterase domain structure from Sulfazecin biosynthetic nonrib... -

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Basic information

Entry
Database: PDB / ID: 8w2c
TitleThioesterase domain structure from Sulfazecin biosynthetic nonribosomal peptide synthetase SulM
ComponentsNon-ribosomal peptide synthetase
KeywordsHYDROLASE / Thioesterase domain / NRPS / nonribosomal peptide synthetase / Sulfazecin
Function / homology
Function and homology information


amide biosynthetic process / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / phosphopantetheine binding / catalytic activity / cytosol
Similarity search - Function
Non-ribosomal peptide synthase / PKS_PP_betabranch / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / Putative AMP-binding domain signature. ...Non-ribosomal peptide synthase / PKS_PP_betabranch / Condensation domain / Condensation domain / Amino acid adenylation domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / Chloramphenicol acetyltransferase-like domain superfamily / AMP-binding, conserved site / 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
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesParaburkholderia acidicola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)61,27010
Polymers60,8132
Non-polymers4578
Water5,098283
1
A: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8028
Polymers30,4071
Non-polymers3957
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4692
Polymers30,4071
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.096, 83.190, 69.380
Angle α, β, γ (deg.)90.000, 101.361, 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
11SERSERGLNGLN(chain 'A' and (resid 2727 through 2817 or resid 2819 through 2979))AA2727 - 281725 - 115
12ASNASNCYSCYS(chain 'A' and (resid 2727 through 2817 or resid 2819 through 2979))AA2819 - 2979117 - 277
21SERSERGLNGLN(chain 'B' and (resid 2727 through 2740 or (resid 2741...BB2727 - 281725 - 115
22ASNASNCYSCYS(chain 'B' and (resid 2727 through 2740 or (resid 2741...BB2819 - 2979117 - 277

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Components

#1: Protein Non-ribosomal peptide synthetase / SulM


Mass: 30406.502 Da / Num. of mol.: 2 / Fragment: Thioesterase domain
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 283 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293.7 K / Method: vapor diffusion / pH: 7 / Details: 100 mM ammonium bromide, and 40% PEG 20,000

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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: Jul 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39586 / % possible obs: 94.3 % / Redundancy: 6.2 % / Biso Wilson estimate: 28.71 Å2 / CC1/2: 0.99 / Net I/σ(I): 11.4
Reflection shellResolution: 1.9→2 Å / Num. unique obs: 5725 / CC1/2: 0.56

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHASERphasing
autoPROC1.0.5data processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.27 Å / SU ML: 0.2568 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5667 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2149 1995 5.05 %
Rwork0.1747 37530 -
obs0.1767 39525 95.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.93 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3820 0 29 283 4132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00943926
X-RAY DIFFRACTIONf_angle_d0.91475344
X-RAY DIFFRACTIONf_chiral_restr0.0564618
X-RAY DIFFRACTIONf_plane_restr0.0064700
X-RAY DIFFRACTIONf_dihedral_angle_d10.02792343
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.38771390.31082637X-RAY DIFFRACTION94.97
1.95-20.2981420.26382658X-RAY DIFFRACTION95.5
2-2.060.30921350.24152563X-RAY DIFFRACTION91.15
2.06-2.120.25291420.22542674X-RAY DIFFRACTION95.49
2.12-2.20.27141430.1952688X-RAY DIFFRACTION96.75
2.2-2.290.25041450.18042708X-RAY DIFFRACTION96.65
2.29-2.390.1931430.16892712X-RAY DIFFRACTION96.32
2.39-2.520.26861360.1732562X-RAY DIFFRACTION91.8
2.52-2.680.21461460.16712727X-RAY DIFFRACTION97.46
2.68-2.880.23531460.17752747X-RAY DIFFRACTION97.8
2.88-3.170.21481440.16972707X-RAY DIFFRACTION96.03
3.17-3.630.21091440.16762698X-RAY DIFFRACTION95.37
3.63-4.580.16281450.14262726X-RAY DIFFRACTION96.99
4.58-42.270.17331450.16362723X-RAY DIFFRACTION94.62
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.93412539933-0.188594225385-0.348029763282.423422301080.4578600616533.009856576760.00387892136639-0.02041239348070.2252569103990.1498931667240.171263869499-0.328972973955-0.3759645072350.664045062026-0.1559118505520.267492510611-0.0793318422481-0.02103899343250.31979089202-0.05511030704540.27366129487618.397626885-13.75966276145.14798392704
20.32612976458-0.5436089522220.1694349976711.05572285963-0.1825305644332.980099502630.00186746976808-0.02796515232010.1278798856270.1451106000140.0725256136141-0.00281709405104-0.380972183758-0.0295617984877-0.1066929385780.3118019869710.04236986625370.01860333635070.190920712716-0.03540622928930.2424600281834.74900305126-15.09659111995.87422887312
33.356840489570.581201597163-2.314924644023.83220357071.159376537379.40969655883-0.234334256407-0.0411760296153-0.409674625069-0.1302151767140.2196560458910.01959380256841.128162295650.54134625254-0.04892169242350.5803139352370.0815232602750.0582293354320.276250357360.0004205565527630.2979739786546.48590584697-35.809656558910.5534615279
41.32282508306-0.003599031248-0.28615596911.39704137060.3472131433814.34352914538-0.0485247784490.01715130990670.05142668819890.0837628259351-0.04739599642650.089900560428-0.233944445338-0.08287069400090.08609357438970.2124024702780.0057750088818-0.001912869710540.186910310699-0.0129962028610.1852874056234.47113942016-18.43024153072.92642050326
55.10910525882-1.131486961170.4881102316419.59523796612-0.6649958211917.117305510440.1599154370560.6492453802940.259409661071-1.03659665254-0.0091656377953-0.388412682487-0.5742010172750.436286074585-0.08557193926410.306801510461-0.07661691239810.05268577972220.410195272247-0.03021030244130.24967908844716.7198745044-15.0520829586-11.3585578187
61.95768897625-0.275447746752-0.7838474848431.66115320515-0.4694173069233.37120967132-0.1692684698020.0397680188661-0.421026376407-0.0235025862363-0.002866222776270.268555921170.580333534183-0.4286135153350.1616385215930.285435813799-0.080389972390.002642556832490.225566700841-0.01913910632780.309200933738-5.21500277287-35.9898901583-29.9818064791
76.353904286372.19762143154-4.637783422342.30629386737-2.006297155027.224086765990.02146888249820.636623700482-0.0875673616546-0.03246542401340.1346398943060.2068334635160.0571994307006-0.85139947508-0.1746910026030.206671301063-0.0105757350017-0.05553534103660.3095779679810.005458549694010.280974946627-9.09822894093-25.8672775592-39.6338340134
85.32183964726-1.64460365004-0.3691926264212.224087690230.5253271421713.699279305310.0749746952681-0.01931622165770.262620129036-0.153723384232-0.0062578548030.2083421629830.0571561289636-0.183002339549-0.06870060605720.196405060128-0.0165877211976-0.005992248749630.1738245225960.01226085579270.239840482048-4.36264557839-23.7250480369-31.2273478731
90.255485876518-0.52461928914-0.4197239479131.348935712140.244673639132.651426186070.156347547482-0.08538047472780.258283668494-0.114979682501-0.0387891559545-0.0310485822924-0.3626059310310.105645683135-0.1460672701240.274820421641-0.01750894427490.00258611904480.1647909299320.008435278263630.2401871782583.70351154184-21.0505387999-33.048692097
104.5523527308-1.17911652745-1.928604561724.27045329274-1.359349638.6814298558-0.004545372066170.03085318418350.142479803561-0.352953984575-0.230987133942-0.368948328420.6456907873970.6359786249850.1473898869380.2717610742590.05497292145470.04070237484880.3102597014140.04915540264510.26874096141718.6757609337-35.8480862105-36.22313584
111.72119761499-0.497857527287-0.760468749721.414340019550.0006905181141623.537326300320.0131889289767-0.0874980552760.139843921296-0.013559241599-0.000532144110122-0.00877234453436-0.1560110576010.175641571999-0.02518006232330.173698706766-0.0471832664867-0.005773536793580.145546301113-0.01693983605090.1730061396986.30395808367-22.9654113825-29.9314172984
125.00749657105-2.81061355382-2.076337557595.410077582732.779028119855.90095282082-0.522840852675-0.868707427334-0.5380783892160.5849627815570.2562341542790.6395028567180.2637176557170.01258164522070.2494498298250.284866891066-0.03416697290570.06519208240320.2840401722810.04701563836220.273551062488-6.16285650135-29.3547211168-15.4437408846
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2727 through 2833 )
2X-RAY DIFFRACTION2chain 'A' and (resid 2834 through 2859 )
3X-RAY DIFFRACTION3chain 'A' and (resid 2860 through 2877 )
4X-RAY DIFFRACTION4chain 'A' and (resid 2878 through 2962 )
5X-RAY DIFFRACTION5chain 'A' and (resid 2963 through 2979 )
6X-RAY DIFFRACTION6chain 'B' and (resid 2726 through 2785 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2786 through 2810 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2811 through 2833 )
9X-RAY DIFFRACTION9chain 'B' and (resid 2834 through 2859 )
10X-RAY DIFFRACTION10chain 'B' and (resid 2860 through 2877 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2878 through 2962 )
12X-RAY DIFFRACTION12chain 'B' and (resid 2963 through 2981 )

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