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- PDB-6vht: Klebsiella oxytoca NpsA N-terminal subdomain in space group C2 -

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Basic information

Entry
Database: PDB / ID: 6vht
TitleKlebsiella oxytoca NpsA N-terminal subdomain in space group C2
ComponentsNpsA Adenylation Domain
KeywordsBIOSYNTHETIC PROTEIN / adenylation / tilivalline / tilimycin / NRPS / nonribosomal peptide synthetase
Function / homology
Function and homology information


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
Similarity search - Domain/homology
BROMIDE ION / Thioester reductase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 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)44,1114
Polymers43,9601
Non-polymers1513
Water2,306128
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


Theoretical massNumber of molelcules
Total (without water)88,2228
Polymers87,9212
Non-polymers3026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3120 Å2
ΔGint-58 kcal/mol
Surface area29210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.597, 60.088, 80.775
Angle α, β, γ (deg.)90.000, 103.542, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein NpsA Adenylation Domain


Mass: 43960.355 Da / Num. of mol.: 1 / Mutation: E312A, E313A, Q314A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: NPSA / Plasmid: pET15 / Details (production host): N-term TEV tag / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2U4DY99
#2: Chemical ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.06 Å3/Da / Density % sol: 40.16 % / Description: 3D
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: well solution: 100 mM HEPES pH 7.5, 150 mM KBr, 30% w/v PEG3350 protein solution (15 mg/mL): 50 mM HEPES pH 8.0, 150 mM NaCl, 0.2 mM TCEP hanging drops: 1 uL protein solution, 1 uL well solution
PH range: 7.5-8

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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 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.84→46.76 Å / Num. obs: 29872 / % possible obs: 96.3 % / Redundancy: 6.8 % / Biso Wilson estimate: 36.28 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.034 / Rrim(I) all: 0.09 / Rsym value: 0.083 / Net I/σ(I): 10.2
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 1552 / CC1/2: 0.335 / Rpim(I) all: 0.886 / Rrim(I) all: 2.286 / Rsym value: 2.103 / % possible all: 96.9

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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: 2vsq

2vsq


Resolution: 1.84→46.76 Å / SU ML: 0.2829 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.2238
RfactorNum. reflection% reflection
Rfree0.2483 1553 5.2 %
Rwork0.2078 --
obs0.21 29864 96.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 52.98 Å2
Refinement stepCycle: LAST / Resolution: 1.84→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 3 128 2888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01172808
X-RAY DIFFRACTIONf_angle_d1.21023834
X-RAY DIFFRACTIONf_chiral_restr0.0703467
X-RAY DIFFRACTIONf_plane_restr0.0068493
X-RAY DIFFRACTIONf_dihedral_angle_d12.5188979
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.90.38821290.34172567X-RAY DIFFRACTION96.53
1.9-1.970.32261390.31772598X-RAY DIFFRACTION96.95
1.97-2.050.29511430.28262564X-RAY DIFFRACTION96.89
2.05-2.140.34491470.26262578X-RAY DIFFRACTION97.04
2.14-2.250.28811320.24922404X-RAY DIFFRACTION97.65
2.25-2.390.28131310.22352329X-RAY DIFFRACTION95.94
2.39-2.580.2511400.22132609X-RAY DIFFRACTION98.18
2.58-2.840.2831470.21882625X-RAY DIFFRACTION98.47
2.84-3.250.27631460.22292650X-RAY DIFFRACTION98.73
3.25-4.090.21411520.18992656X-RAY DIFFRACTION99.08
4.09-46.760.2161470.1742731X-RAY DIFFRACTION99.41
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)
14.587663268230.05263828590640.4187907739962.987252042180.2423081341644.639961777620.1968981630270.5461648324440.485867058972-0.543254085807-0.280047475007-0.280183866372-0.4703954610410.4407214681080.07815938851960.5547799366220.1729691275110.09080957109580.4263063310960.09464673801370.32990049316325.544745707738.915094244513.1565253661
21.743659632590.3043140396140.05053351747861.961418223310.4015923477393.263840889880.2429879892940.106329973509-0.0328869965164-0.188715503056-0.1600793764190.1078720713460.364458728099-0.0208791898288-0.07071371449140.3397983783750.119335940358-0.03623467055970.327492274301-0.0001942124106330.23223131446722.040956002922.913079301623.0691121104
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 125 )
2X-RAY DIFFRACTION2chain 'A' and (resid 126 through 401 )

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