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- PDB-6vhv: Klebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN -

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Basic information

Entry
Database: PDB / ID: 6vhv
TitleKlebsiella oxytoca NpsA in complex with 3-hydroxyanthranilyl-AMSN
ComponentsNpsA Adenylation Domain
KeywordsBIOSYNTHETIC PROTEIN / adenylation / tilivalline / tilimycin / NRPS / nonribosomal peptide synthetase
Function / homology
Function and homology information


ANL, C-terminal domain / ANL, N-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-QXG / Thioester reductase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.89 Å
AuthorsKreitler, D.F. / 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: Acs Infect Dis. / Year: 2020
Title: Biosynthesis, Mechanism of Action, and Inhibition of the Enterotoxin Tilimycin Produced by the Opportunistic PathogenKlebsiella oxytoca.
Authors: Alexander, E.M. / Kreitler, D.F. / Guidolin, V. / Hurben, A.K. / Drake, E. / Villalta, P.W. / Balbo, S. / Gulick, A.M. / Aldrich, C.C.
History
DepositionJan 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.2Oct 11, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NpsA Adenylation Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,0352
Polymers55,5551
Non-polymers4801
Water1448
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NpsA Adenylation Domain
hetero molecules

A: NpsA Adenylation Domain
hetero molecules

A: NpsA Adenylation Domain
hetero molecules

A: NpsA Adenylation Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,1418
Polymers222,2194
Non-polymers1,9224
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area6490 Å2
ΔGint-39 kcal/mol
Surface area78060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.689, 87.817, 165.778
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein NpsA Adenylation Domain


Mass: 55554.848 Da / Num. of mol.: 1 / Mutation: E312A, E313A, Q314A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Strain: NPSA / Gene: AGF18_11095 / Plasmid: pET15 / Details (production host): N-term TEV tag / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U4DY99
#2: Chemical ChemComp-QXG / 5'-{[(2-amino-3-hydroxybenzene-1-carbonyl)sulfamoyl]amino}-5'-deoxyadenosine


Mass: 480.455 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H20N8O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 6.6
Details: well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0. ...Details: well solution: 400 mM imidazole pH 6.6, 10% w/v PEG8000/10000/12000/20000, 2.5% w/v 1,3-dimethylimidazolium dimethyl phosphate protein solution (16 mg/mL): 10 mM HEPES pH 8.0, 25 mM NaCl, 0.4 mM TCEP, 5 mM 3HA-AMSN droplet: 2 uL protein solution, 1 uL well solution

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 2.89→68.1 Å / Num. obs: 12516 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 86.74 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.063 / Rrim(I) all: 0.163 / Rsym value: 0.149 / Net I/σ(I): 9.4
Reflection shellResolution: 2.89→2.95 Å / Redundancy: 6.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 605 / CC1/2: 0.412 / Rpim(I) all: 0.858 / Rrim(I) all: 2.261 / Rsym value: 2.088 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
autoPROC1.0.5 (20181127)data scaling
PHASERphasing
Cootmodel building
PHENIX1.15_3459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vhu

6vhu


Resolution: 2.89→68.1 Å / SU ML: 0.508 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.174
RfactorNum. reflection% reflection
Rfree0.262 604 4.83 %
Rwork0.2176 --
obs0.2198 12507 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 97.58 Å2
Refinement stepCycle: LAST / Resolution: 2.89→68.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 33 8 3713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00383779
X-RAY DIFFRACTIONf_angle_d0.55585152
X-RAY DIFFRACTIONf_chiral_restr0.0467611
X-RAY DIFFRACTIONf_plane_restr0.0046661
X-RAY DIFFRACTIONf_dihedral_angle_d15.58261351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.89-3.190.41111320.33622924X-RAY DIFFRACTION99.77
3.19-3.650.30751640.26772933X-RAY DIFFRACTION99.94
3.65-4.590.23241450.19562969X-RAY DIFFRACTION99.81
4.59-68.10.24291630.19523077X-RAY DIFFRACTION99.72
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)
15.773514782780.4057376595810.7390041663614.01927746915-0.6862205764883.545953084950.0375440742393-0.5312330712740.4587652707230.659080132837-0.157571493826-0.0861410155573-0.03626645563840.0989183154913-1.82576992916E-80.581030239635-0.04834639762760.006264564359480.6486559058210.01163111148570.54415926631423.837896539633.406946792343.0180593144
23.6766828077-0.1571090706261.451528959093.439189380780.492618591032.546617830480.07463597781140.0637341602184-0.08973718727960.119249165035-0.132013628807-0.09983799268680.816915604990.08254543954132.14344471241E-70.6703462145220.01838539481540.09674193229870.5480860607980.07245507406990.47760628903412.057255714323.686862196127.9642400751
32.05722648299-0.5129783735640.1238104228032.22721414949-0.6452185980462.58184402036-0.3203651748590.6433569491790.548719346354-0.905882392658-0.02422260091460.203857512316-0.2134413977470.311722169829-1.52144422289E-70.680505192038-0.069521703787-0.0490818323750.711355460180.1756501792080.76775676413811.119894105738.790318588916.0625057481
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 158 )
2X-RAY DIFFRACTION2chain 'A' and (resid 159 through 285 )
3X-RAY DIFFRACTION3chain 'A' and (resid 286 through 375 )

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