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- PDB-8k4r: Structure of VinM-VinL complex -

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Basic information

Entry
Database: PDB / ID: 8k4r
TitleStructure of VinM-VinL complex
Components
  • Acyl-carrier-protein
  • Non-ribosomal peptide synthetase
KeywordsLIGASE / Complex / Adenylation enzyme / ATP / Carrier protein / Biosynthesis
Function / homology
Function and homology information


D-alanine:D-alanyl carrier protein ligase-like / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Phosphopantetheine attachment site / Phosphopantetheine attachment site. / Phosphopantetheine attachment site ...D-alanine:D-alanyl carrier protein ligase-like / ANL, N-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / 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
Similarity search - Domain/homology
Chem-VPI / Non-ribosomal peptide synthetase / Acyl-carrier-protein
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMiyanaga, A. / Nagata, K. / Nakajima, J. / Chisuga, T. / Kudo, F. / Eguchi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H02911 Japan
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Structural Basis of Amide-Forming Adenylation Enzyme VinM in Vicenistatin Biosynthesis.
Authors: Miyanaga, A. / Nagata, K. / Nakajima, J. / Chisuga, T. / Kudo, F. / Eguchi, T.
History
DepositionJul 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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: Acyl-carrier-protein
C: Non-ribosomal peptide synthetase
D: Acyl-carrier-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,6248
Polymers139,6994
Non-polymers9254
Water77543
1
A: Non-ribosomal peptide synthetase
B: Acyl-carrier-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3124
Polymers69,8502
Non-polymers4622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Non-ribosomal peptide synthetase
D: Acyl-carrier-protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3124
Polymers69,8502
Non-polymers4622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.501, 72.987, 80.209
Angle α, β, γ (deg.)94.180, 90.870, 103.340
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEUAA5 - 52221 - 538
21ASPASPLEULEUCC5 - 52221 - 538
12METMETGLNGLNBB1 - 7621 - 96
22METMETGLNGLNDD1 - 7621 - 96

NCS ensembles :
ID
1
2

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Components

#1: Protein Non-ribosomal peptide synthetase / VinM


Mass: 58061.473 Da / Num. of mol.: 2 / Mutation: D223C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinM / Plasmid: pCold I / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY3
#2: Protein Acyl-carrier-protein / VinL


Mass: 11788.082 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Gene: vinL / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q76KY4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-VPI / [(3~{R})-4-[[3-(6-acetamidohexylamino)-3-oxidanylidene-propyl]amino]-2,2-dimethyl-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate


Mass: 439.441 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H34N3O8P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.3 Å3/Da / Density % sol: 46.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES-Na, sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 17, 2022
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 54087 / % possible obs: 97.9 % / Redundancy: 3.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Net I/σ(I): 11.2
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.626 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4443 / CC1/2: 0.826 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→46.04 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.931 / SU B: 22.685 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2508 2703 5 %RANDOM
Rwork0.2067 ---
obs0.2089 51384 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 117.73 Å2 / Biso mean: 62.016 Å2 / Biso min: 33.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.94 Å20.57 Å2-1.12 Å2
2---0.65 Å2-0.62 Å2
3----0.3 Å2
Refinement stepCycle: final / Resolution: 2.3→46.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8624 0 58 43 8725
Biso mean--62.7 50.35 -
Num. residues----1124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0138899
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178278
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.65412145
X-RAY DIFFRACTIONr_angle_other_deg1.6391.58219040
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.15251113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.53520.144486
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.3151286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1191588
X-RAY DIFFRACTIONr_chiral_restr0.0630.21133
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210121
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022009
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A142510.07
12C142510.07
21B23820.04
22D23820.04
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 212 -
Rwork0.294 3799 -
all-4011 -
obs--97.26 %
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)
10.32690.21390.07460.6216-0.00010.3398-0.08350.111-0.0305-0.08960.0858-0.01750.01820.0374-0.00220.0634-0.0184-0.01190.54-0.20360.08521.3441.342-3.43
21.7661-0.4564-0.51280.67960.29281.75940.2322-0.1358-0.1806-0.1608-0.02870.25370.4044-0.1714-0.20340.2091-0.0825-0.15770.6465-0.13980.2055-15.354-1.56717.879
30.22090.09720.10311.07560.94221.9450.0596-0.0846-0.0213-0.1086-0.16290.0067-0.3597-0.33480.10330.11680.0439-0.03650.5668-0.17560.06750.69631.26839.723
42.7737-1.9785-0.57631.94660.0421.81420.0581-0.38530.22120.17640.0796-0.2883-0.11050.4562-0.13770.0917-0.0843-0.05310.6485-0.19310.140422.32310.08733.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 524
2X-RAY DIFFRACTION2B1 - 77
3X-RAY DIFFRACTION3C5 - 522
4X-RAY DIFFRACTION4D1 - 78

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