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- PDB-6n8e: Crystal structure of holo-ObiF1, a five domain nonribosomal pepti... -

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Basic information

Entry
Database: PDB / ID: 6n8e
TitleCrystal structure of holo-ObiF1, a five domain nonribosomal peptide synthetase from Burkholderia diffusa
Componentsholo-ObiF1
KeywordsHYDROLASE / NRPS / beta-lactone / module / thioesterase
Function / homology
Function and homology information


hydrolase activity, acting on ester bonds / biosynthetic process / phosphopantetheine binding / metal ion binding
Similarity search - Function
MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Alpha/beta hydrolase family ...MbtH-like domain / MbtH-like domain superfamily / MbtH-like protein / MbtH-like protein / Polyketide synthase, thioesterase domain / Thioesterase / Condensation domain / Condensation domain / Amino acid adenylation domain / Alpha/beta hydrolase family / ANL, N-terminal 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 / Alpha/beta hydrolase fold-1 / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site / ACP-like superfamily / Phosphopantetheine binding ACP domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
dimethyl hydrogen phosphate / 4-(4-nitrophenyl)-L-threonine / 4'-PHOSPHOPANTETHEINE / PHOSPHATE ION / holo-ObiF1
Similarity search - Component
Biological speciesBurkholderia diffusa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKreitler, D.F. / Wencewicz, T.A. / Gulick, A.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM116957 United States
CitationJournal: Nat Commun / Year: 2019
Title: The structural basis of N-acyl-alpha-amino-beta-lactone formation catalyzed by a nonribosomal peptide synthetase.
Authors: Kreitler, D.F. / Gemmell, E.M. / Schaffer, J.E. / Wencewicz, T.A. / Gulick, A.M.
History
DepositionNov 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: holo-ObiF1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,2667
Polymers152,3161
Non-polymers9506
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.325, 154.345, 183.905
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein holo-ObiF1


Mass: 152316.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia diffusa (bacteria) / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5H1ZR44*PLUS

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Non-polymers , 6 types, 17 molecules

#2: Chemical ChemComp-PNS / 4'-PHOSPHOPANTETHEINE


Mass: 358.348 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23N2O7PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-KFG / dimethyl hydrogen phosphate


Mass: 126.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7O4P
#4: Chemical ChemComp-KFJ / 4-(4-nitrophenyl)-L-threonine


Mass: 240.213 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12N2O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.79 Å3/Da / Density % sol: 67.54 % / Description: 3D bricks with facets
Crystal growTemperature: 287 K / Method: microbatch / pH: 6.8
Details: well solution: 90 mM HEPES pH 6.8, 5% w/v 1,3-dimethylimidazolium dimethyl phosphate, 27% w/v PEG3350; protein sample: 25 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5% v/v glycerol, 36.5 ...Details: well solution: 90 mM HEPES pH 6.8, 5% w/v 1,3-dimethylimidazolium dimethyl phosphate, 27% w/v PEG3350; protein sample: 25 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5% v/v glycerol, 36.5 mg/mL holo-ObiF1; drop composition: 2 uL protein: 1 uL well solution under paraffin oil

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 3→39.7034 Å / Num. obs: 47131 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 64.97 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.041 / Rrim(I) all: 0.105 / Rsym value: 0.096 / Net I/σ(I): 11.4
Reflection shellResolution: 3→3.11 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4545 / CC1/2: 0.938 / Rpim(I) all: 0.171 / Rrim(I) all: 0.442 / Rsym value: 0.407 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U89, 5T3D, 3FLB

5u89

5t3d

3flb


Resolution: 3→39.703 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 25.77
RfactorNum. reflection% reflection
Rfree0.24 1998 4.25 %
Rwork0.2103 --
obs0.2116 47061 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 177.57 Å2 / Biso mean: 79.0011 Å2 / Biso min: 26.77 Å2
Refinement stepCycle: final / Resolution: 3→39.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9937 0 93 11 10041
Biso mean--88.93 33.5 -
Num. residues----1332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3-3.0750.36931400.311331573297
3.075-3.15810.36791410.292731753316
3.1581-3.2510.32761420.266831923334
3.251-3.35590.24991410.255431703311
3.3559-3.47580.27821400.250931703310
3.4758-3.61480.26721400.236931783318
3.6148-3.77920.30031420.227131983340
3.7792-3.97830.22051410.209131833324
3.9783-4.22730.24711430.203732213364
4.2273-4.55330.21361430.181632203363
4.5533-5.01070.20341430.167532303373
5.0107-5.73390.22061440.192332533397
5.7339-7.2170.23971450.20732863431
7.217-39.70680.1771530.180934303583
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)
12.4259-0.20270.08252.3184-0.30971.87740.0358-0.0103-0.003-0.01870.0166-0.18960.02380.4046-0.0090.2849-0.0742-0.00480.498-0.01020.379-18.482-41.9077.755
21.109-0.1948-0.1031.02130.62732.29170.0248-0.02070.070.0895-0.00410.07830.1186-0.28470.00140.3765-0.1056-0.00170.4026-0.00740.4354-35.054-33.78522.54
31.6778-0.424-0.23342.35561.06961.5236-0.03-0.15020.21110.32080.1262-0.10360.24410.1187-0.10740.46980.015-0.01870.488-0.08330.4497-25.278-33.2139.511
41.9111-1.0396-0.75142.72511.13662.3755-0.1318-0.0066-0.120.48850.2768-0.18120.25920.1932-0.1170.57930.1233-0.09690.4712-0.15870.464-37.69612.60675.784
51.5988-0.1933-0.62413.43250.62581.90450.07850.27170.0031-0.25810.2391-0.81550.09330.5231-0.27680.58610.0936-0.04940.8556-0.30360.7157-20.3327.9360.843
61.2391-0.23390.39883.55432.18872.8573-0.2199-0.09720.30710.25550.2768-0.3458-0.02730.4956-0.07740.5440.0544-0.05060.5446-0.1780.61-29.138-11.6755.233
73.617-0.8188-1.86512.4130.51064.56420.4804-0.20110.983-0.1821-0.2129-0.2702-0.5591-0.3488-0.26350.433-0.01770.09490.4791-0.17280.7741.869-16.53821.075
82.8427-0.732-0.99181.70760.7072.53910.1386-0.91640.62340.24530.0289-0.1875-0.09440.4015-0.14730.389-0.10120.00310.825-0.14220.53711.548-25.08928.432
92.5097-0.3014-0.64691.5266-1.00022.0186-0.3381-0.29740.12240.42520.22320.28690.3953-0.41640.12370.7353-0.09410.12540.6254-0.20450.5756-45.122-19.58455.082
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 4:169 )A4 - 169
2X-RAY DIFFRACTION2( CHAIN A AND RESID 170:379 )A170 - 379
3X-RAY DIFFRACTION3( CHAIN A AND RESID 380:453 )A380 - 453
4X-RAY DIFFRACTION4( CHAIN A AND RESID 454:616 )A454 - 616
5X-RAY DIFFRACTION5( CHAIN A AND RESID 617:776 )A617 - 776
6X-RAY DIFFRACTION6( CHAIN A AND RESID 777:870 )A777 - 870
7X-RAY DIFFRACTION7( CHAIN A AND RESID 1059:1131 )A1059 - 1131
8X-RAY DIFFRACTION8( CHAIN A AND RESID 1132:1303 )A1132 - 1303
9X-RAY DIFFRACTION9( CHAIN A AND RESID 1313:1370 )A1313 - 1370

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