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- PDB-3wv4: Crystal structure of VinN -

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Basic information

Entry
Database: PDB / ID: 3wv4
TitleCrystal structure of VinN
ComponentsNon-ribosomal peptide synthetase
KeywordsLIGASE / Five-layered alpha-beta-alpha-beta-alpha sandwich fold / ATP binding
Function / homology
Function and homology information


ligase activity, forming carbon-sulfur bonds
Similarity search - Function
ANL, N-terminal domain / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsMiyanaga, A. / Cieslak, J. / Shinohara, Y. / Kudo, F. / Eguchi, T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The crystal structure of the adenylation enzyme VinN reveals a unique beta-amino acid recognition mechanism
Authors: Miyanaga, A. / Cieslak, J. / Shinohara, Y. / Kudo, F. / Eguchi, T.
History
DepositionMay 15, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)96,3492
Polymers96,3492
Non-polymers00
Water3,441191
1
A: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)48,1751
Polymers48,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-ribosomal peptide synthetase


Theoretical massNumber of molelcules
Total (without water)48,1751
Polymers48,1751
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.190, 109.820, 201.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 24 - 423 / Label seq-ID: 40 - 439

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Non-ribosomal peptide synthetase


Mass: 48174.551 Da / Num. of mol.: 2 / Fragment: N-terminal domain UNP residues 1-379
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces halstedii (bacteria) / Strain: HC34 / Gene: vinN / Plasmid: pCold I / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q76KY2, Ligases; Forming carbon-sulfur bonds; Acid-thiol ligases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.2M sodium acetate, 30% polyethylene glycol 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2013
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 2.15→50.37 Å / Num. all: 49335 / Num. obs: 44155 / % possible obs: 89.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.21 Å / % possible all: 83.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AU9

3au9


Resolution: 2.15→50.37 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 13.005 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.267 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES: WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2449 2218 5 %RANDOM
Rwork0.2017 41905 --
obs0.2039 41905 89.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.66 Å2 / Biso mean: 43.753 Å2 / Biso min: 19.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å2-0 Å2-0 Å2
2--0.87 Å20 Å2
3----4.35 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5845 0 0 191 6036
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195973
X-RAY DIFFRACTIONr_bond_other_d0.0050.025722
X-RAY DIFFRACTIONr_angle_refined_deg1.711.978133
X-RAY DIFFRACTIONr_angle_other_deg1.158313135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0675756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.04922.764246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.35315935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9151550
X-RAY DIFFRACTIONr_chiral_restr0.0970.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216704
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021322
Refine LS restraints NCS

Ens-ID: 1 / Number: 21703 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.148→2.204 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 162 -
Rwork0.299 2822 -
all-2984 -
obs--82.48 %
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)
10.6304-0.08250.53960.6968-0.21430.51790.0240.0180.11840.1527-0.1437-0.04320.00260.01560.11970.0542-0.0488-0.0380.06210.00870.198920.568621.624980.3393
20.77690.34560.60971.322-0.43770.92820.01-0.0726-0.18750.24070.0715-0.2518-0.1051-0.1696-0.08150.0603-0.0156-0.05570.11720.02070.193326.621259.559271.9101
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 425
2X-RAY DIFFRACTION1A501 - 598
3X-RAY DIFFRACTION2B24 - 423
5X-RAY DIFFRACTION2B501 - 593

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