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- PDB-3wv5: Complex structure of VinN with 3-methylaspartate -

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Basic information

Entry
Database: PDB / ID: 3wv5
TitleComplex structure of VinN with 3-methylaspartate
ComponentsNon-ribosomal peptide synthetase
KeywordsLIGASE / Five-layered alpha-beta-alpha-beta-alpha sandwich fold / ATP binding
Function / homology
Function and homology information


acid-thiol ligase activity
Similarity search - Function
: / ANL, N-terminal domain / ANL, N-terminal domain / AMP-dependent synthetase/ligase / AMP-binding enzyme / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S,3S)-3-methyl-aspartic acid / Non-ribosomal peptide synthetase
Similarity search - Component
Biological speciesStreptomyces halstedii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 ...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_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)96,6434
Polymers96,3492
Non-polymers2942
Water3,657203
1
A: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3222
Polymers48,1751
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Non-ribosomal peptide synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3222
Polymers48,1751
Non-polymers1471
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.660, 109.410, 200.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-774-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / Refine code: _

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLYGLYAA24 - 42440 - 440
22AS2ASBB - D24 - 60140

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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: Chemical ChemComp-2AS / (2S,3S)-3-methyl-aspartic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.29 Å3/Da / Density % sol: 46.34 %
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, 100mM DL-threo-beta-methylaspartate, 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: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 17, 2013
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: 2.2→37.44 Å / Num. all: 45284 / Num. obs: 44288 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 93.6

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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 3WV4

3wv4


Resolution: 2.2→37.44 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.927 / SU B: 14.395 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24514 2233 5 %RANDOM
Rwork0.20512 ---
obs0.20714 42011 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.959 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å20 Å20 Å2
2---1.04 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5690 0 20 203 5913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195833
X-RAY DIFFRACTIONr_bond_other_d0.0050.025579
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.977941
X-RAY DIFFRACTIONr_angle_other_deg1.147312806
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3925736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.76122.857238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.54515910
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7361546
X-RAY DIFFRACTIONr_chiral_restr0.10.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216541
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021289
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Number: 21113 / 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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 172 -
Rwork0.266 2901 -
obs--93.29 %
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)
10.79540.02470.51711.2326-0.49130.56050.0877-0.01380.13710.1856-0.17160.02570.01330.03070.08390.185-0.0523-0.04020.1843-0.00590.091921.049521.36879.6586
21.42091.04651.08662.9073-0.07321.2101-0.03740.023-0.41930.43290.3275-0.4592-0.1774-0.1926-0.29010.1486-0.0015-0.05540.30840.01090.149826.052859.920971.0437
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 425
2X-RAY DIFFRACTION1A601
3X-RAY DIFFRACTION1A701 - 796
4X-RAY DIFFRACTION2B24 - 423
5X-RAY DIFFRACTION2B601
6X-RAY DIFFRACTION2B701 - 807

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