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- PDB-2vsq: Structure of surfactin A synthetase C (SrfA-C), a nonribosomal pe... -

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Basic information

Entry
Database: PDB / ID: 2vsq
TitleStructure of surfactin A synthetase C (SrfA-C), a nonribosomal peptide synthetase termination module
ComponentsSURFACTIN SYNTHETASE SUBUNIT 3
KeywordsLIGASE / PEPTIDYL CARRIER PROTEIN / LIGASE PHOSPHOPROTEIN / TERMINATION MODULE / PHOSPHOPANTETHEINE / NONRIBOSOMAL PEPTIDE SYNTHESIS / SYNTHETASE / ADENYLATION / SPORULATION / ANTIBIOTIC BIOSYNTHESIS / ENZYMATIC ASSEMBLY LINE / SURFACTIN A / CONDENSATION / THIOESTERASE
Function / homology
Function and homology information


amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / sporulation resulting in formation of a cellular spore / phosphopantetheine binding / ligase activity / antibiotic biosynthetic process / cytoplasm
Similarity search - Function
Nonribosomal peptide synthetase, condensation domain / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / ACP-like / ANL, C-terminal domain / Thioesterase / Thioesterase domain ...Nonribosomal peptide synthetase, condensation domain / Rossmann fold - #980 / Luciferase; domain 3 / Luciferase; Domain 3 / Chloramphenicol Acetyltransferase / Chloramphenicol acetyltransferase-like domain / ACP-like / ANL, C-terminal domain / Thioesterase / Thioesterase domain / Condensation domain / Condensation domain / Amino acid adenylation domain / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / 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 / GMP Synthetase; Chain A, domain 3 / 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, catalytic domain / Alpha/Beta hydrolase fold / Roll / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LEUCINE / Surfactin synthase subunit 3
Similarity search - Component
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsTanovic, A. / Samel, S.A. / Essen, L.-O. / Marahiel, M.A.
CitationJournal: Science / Year: 2008
Title: Crystal structure of the termination module of a nonribosomal peptide synthetase.
Authors: Tanovic, A. / Samel, S.A. / Essen, L.O. / Marahiel, M.A.
History
DepositionApr 29, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection / Database references
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_radiation
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_radiation.pdbx_diffrn_protocol
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SURFACTIN SYNTHETASE SUBUNIT 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,6683
Polymers147,4411
Non-polymers2272
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.106, 106.562, 92.401
Angle α, β, γ (deg.)90.00, 97.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SURFACTIN SYNTHETASE SUBUNIT 3 / SURFACTIN A SYNTHETASE C


Mass: 147440.547 Da / Num. of mol.: 1
Fragment: TERMINATION MODULE OF SURFACTIN A BIOSYNTHESIS CLUSTER, RESIDUES 1-1009,1015-1274
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS (bacteria) / Plasmid: PTRCHIS2-TOPO_SRFA-C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / Variant (production host): PREP4 / References: UniProt: Q08787
#2: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 1003 TO ALA
Nonpolymer detailsL-LEUCINE (LEU): L-LEUCINE IS BOUND TO THE SUBSTRATE BINDING SITE OF THE A DOMAIN OF SRFA-C.
Sequence detailsPLEASE NOTE THAT THE GENBANK ENTRY CONTAINS THE SEQUENCE OF B. SUBTILIS STRAIN 168, WHEREAS THE ...PLEASE NOTE THAT THE GENBANK ENTRY CONTAINS THE SEQUENCE OF B. SUBTILIS STRAIN 168, WHEREAS THE RECOMBINANT PROTEIN' S SOURCE IS B. SUBTILIS STRAIN ATCC 21332. THEREFORE THERE ARE THE FOLLOWING AMINO ACID EXCHANGES COMPARED TO THE AFOREMENTIONED GENBANK ENTRY. P26A, T33S, L235P. RESIDUES 1010-1014, VPHQQ, ARE REPLACED BY ASRIKK DUE TO A FRAME SHIFT. THE PROTEIN CONTAINS A S1003A POINT MUTATION AND 29 AMINO ACIDS THAT ARE DERIVED FROM THE VECTOR'S MULTIPLE CLONING SITE, C-MYC EPITOPE SEQUENCE, A LINKER AND A HEXA- HISTIDINE TAG.

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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: 2.87 Å3/Da / Density % sol: 56.76 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M MGCL2, 0.05 M HEPES (PH 7.5), 15 % (W/V) PEG 2000

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONSLS X06SA20.9794, 0.9792, 0.9717
Detector
TypeIDDetectorDate
ADSC CCD1CCDJul 14, 2007
2
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MADMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
20.97941
30.97921
40.97171
ReflectionResolution: 2.6→82.5 Å / Num. obs: 45564 / % possible obs: 93 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 79.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.9
Reflection shellResolution: 2.6→2.67 Å / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2 / % possible all: 68

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MAD
Starting model: PDB ENTRIES 1AMU AND 2JGP

1amu

2jgp


Resolution: 2.6→82.5 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 28.59 / SU ML: 0.284 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.907 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1156-1160, 1175-1181 AND 1202-1206 ARE DISORDERED AND MISSING IN THE SRFA-C STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1040 2.3 %RANDOM
Rwork0.213 ---
obs0.215 44479 93.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.59 Å20 Å2-0.03 Å2
2---0.53 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.6→82.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10056 0 14 39 10109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02210282
X-RAY DIFFRACTIONr_bond_other_d0.0010.026915
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.96413938
X-RAY DIFFRACTIONr_angle_other_deg0.878316908
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.01451269
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32724.847489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.167151770
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2641552
X-RAY DIFFRACTIONr_chiral_restr0.0710.21548
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022025
X-RAY DIFFRACTIONr_nbd_refined0.2280.22646
X-RAY DIFFRACTIONr_nbd_other0.1880.27308
X-RAY DIFFRACTIONr_nbtor_refined0.1860.25005
X-RAY DIFFRACTIONr_nbtor_other0.0890.25551
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2309
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2020.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4631.56805
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.765210215
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.92934310
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.4084.53723
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.436 50
Rwork0.324 2207
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)
12.7182-1.9803-2.07864.62562.81523.5903-0.0056-0.0288-0.097-0.15920.1647-0.1555-0.05430.2639-0.1591-0.249-0.0111-0.0186-0.2598-0.0081-0.2021-79.8459-12.8102-58.4623
26.585-1.48511.40032.60280.12642.08230.1471-0.0394-0.3622-0.0105-0.06410.01110.1163-0.095-0.083-0.2034-0.0453-0.0482-0.3071-0.0082-0.1848-62.2106-8.9218-35.482
34.43091.62680.8522.3867-0.05321.57850.419-0.3345-0.60830.5141-0.2007-0.42970.11740.211-0.2183-0.16340.0773-0.1122-0.17820.1253-0.1878-21.5382-1.2269-14.609
40.8527-3.14331.117511.6508-3.63555.1314-0.4399-0.26180.87310.3485-0.073-1.034-1.13570.44330.51290.1245-0.0655-0.14580.20740.05670.4929-45.025919.2204-25.7638
53.17893.55732.229514.04075.52496.116-1.03881.0971-0.5596-2.01720.784-0.24720.56670.55860.25480.7253-0.14950.35590.0841-0.10120.2924-61.307318.5036-52.43
67.1353-1.1456-2.36685.15931.68683.34930.3279-0.67510.58340.7886-0.11750.7345-0.2381-0.4767-0.21040.8566-0.13350.39250.98370.00480.2602-38.76963.8963-75.8345
78.66831.0708-2.843916.29440.500830.369-0.55990.88050.9327-0.7583-0.40550.9164-0.8094-0.8210.96540.0770.15970.09370.12140.2790.1165-10.22758.1815-64.2136
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 195
2X-RAY DIFFRACTION1A283 - 298
3X-RAY DIFFRACTION1A358 - 381
4X-RAY DIFFRACTION2A196 - 282
5X-RAY DIFFRACTION2A299 - 357
6X-RAY DIFFRACTION2A382 - 431
7X-RAY DIFFRACTION3A432 - 858
8X-RAY DIFFRACTION4A859 - 964
9X-RAY DIFFRACTION5A965 - 1045
10X-RAY DIFFRACTION6A1046 - 1270
11X-RAY DIFFRACTION7A1271 - 1290

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