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- PDB-6vhu: Klebsiella oxytoca NpsA N-terminal subdomain in space group P21 -

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Basic information

Entry
Database: PDB / ID: 6vhu
TitleKlebsiella oxytoca NpsA N-terminal subdomain in space group P21
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: 1.6 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
B: NpsA Adenylation Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,52612
Polymers87,9212
Non-polymers60510
Water9,836546
1
A: NpsA Adenylation Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2217
Polymers43,9601
Non-polymers2616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NpsA Adenylation Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3055
Polymers43,9601
Non-polymers3454
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.949, 59.114, 80.408
Angle α, β, γ (deg.)90.000, 101.124, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NpsA Adenylation Domain


Mass: 43960.355 Da / Num. of mol.: 2 / 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

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Non-polymers , 5 types, 556 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 546 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.91 Å3/Da / Density % sol: 35.55 % / 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: 7.5-8.0

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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
RadiationMonochromator: 1.03322 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03322 Å / Relative weight: 1
ReflectionResolution: 1.6→70.6 Å / Num. obs: 84862 / % possible obs: 96.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 20.6 Å2 / CC1/2: 0.995 / Rpim(I) all: 0.051 / Rrim(I) all: 0.132 / Rsym value: 0.121 / Net I/σ(I): 8.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 3365 / CC1/2: 0.381 / Rpim(I) all: 0.805 / Rrim(I) all: 1.944 / Rsym value: 1.757 / % possible all: 77.5

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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: 6vht

6vht


Resolution: 1.6→70.6 Å / SU ML: 0.2036 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1528
RfactorNum. reflection% reflection
Rfree0.2184 4200 4.95 %
Rwork0.188 --
obs0.1895 84837 96.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6→70.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5759 0 24 546 6329
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01325988
X-RAY DIFFRACTIONf_angle_d0.93128181
X-RAY DIFFRACTIONf_chiral_restr0.0666975
X-RAY DIFFRACTIONf_plane_restr0.00621057
X-RAY DIFFRACTIONf_dihedral_angle_d13.06152164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.32721260.30022061X-RAY DIFFRACTION75.73
1.62-1.630.35911050.28872340X-RAY DIFFRACTION82.52
1.63-1.650.29851380.29082503X-RAY DIFFRACTION92.89
1.65-1.680.29521400.26972640X-RAY DIFFRACTION94.4
1.68-1.70.28821460.25382671X-RAY DIFFRACTION96.51
1.7-1.720.30131140.24262720X-RAY DIFFRACTION96.76
1.72-1.750.2641330.24152662X-RAY DIFFRACTION96.51
1.75-1.770.25461420.23852678X-RAY DIFFRACTION97.11
1.77-1.80.27371450.23642727X-RAY DIFFRACTION97.19
1.8-1.830.28511200.23282673X-RAY DIFFRACTION96.64
1.83-1.860.25641250.23392719X-RAY DIFFRACTION97.43
1.86-1.890.35961250.23342744X-RAY DIFFRACTION97.75
1.89-1.930.26891400.22392689X-RAY DIFFRACTION97.45
1.93-1.970.2411310.20912713X-RAY DIFFRACTION97.3
1.97-2.010.24211410.19712715X-RAY DIFFRACTION97.47
2.01-2.060.20991630.19432709X-RAY DIFFRACTION97.95
2.06-2.110.22221440.19282726X-RAY DIFFRACTION97.99
2.11-2.170.21441370.19112738X-RAY DIFFRACTION98.06
2.17-2.230.21031540.18612685X-RAY DIFFRACTION98.17
2.23-2.30.21431430.18242733X-RAY DIFFRACTION98.39
2.3-2.390.21741440.18272757X-RAY DIFFRACTION98.61
2.39-2.480.20991640.18482730X-RAY DIFFRACTION98.64
2.48-2.60.2271480.18372740X-RAY DIFFRACTION98.37
2.6-2.730.22151620.18662729X-RAY DIFFRACTION99.11
2.73-2.90.19271450.18052773X-RAY DIFFRACTION98.88
2.9-3.130.19421470.18032793X-RAY DIFFRACTION99.16
3.13-3.440.2261330.1612788X-RAY DIFFRACTION99.22
3.44-3.940.14631580.15652775X-RAY DIFFRACTION99.32
3.94-4.960.18111420.15292820X-RAY DIFFRACTION99.46
4.96-70.60.25291450.19342886X-RAY DIFFRACTION99.38
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)
12.70702730680.126122542357-0.3782779480081.70828347439-0.07087094740511.971970982430.0394175820274-0.1149185715370.1422201212470.146201576922-0.0415004974467-0.163184570159-0.1698933530380.149802019516-0.009089777760360.157576675808-0.0476292068146-0.0361656935250.125856808851-0.01027757470850.14102439839729.767456401711.937628827826.7131792174
23.38531054536-0.0811118502148-0.7113225320223.8923942241-0.1971880770190.7914815699230.09786281138520.2378529424880.174872287248-0.257859289826-0.02571013974650.488347694496-0.168314238045-0.432220962425-0.06946925607490.2150597238880.0262586011994-0.00885544520660.266282637926-0.0005886992235780.2131257699110.132165190510.189857726225.1753248295
31.27438693275-1.543918961941.318167092413.07002679416-1.88533886091.65627154176-0.0419012145508-0.2206760097640.6800354762720.461211430787-0.171143950111-0.37122454411-0.2346924884940.02921473691950.2276991485990.268811976506-0.0403739844506-0.0500558627930.180511935652-0.04137392058140.13932132991124.011057864615.430176275733.9714127063
40.369621498699-0.0753743997768-0.05408893956091.04514194157-0.3158364533221.82781921610.04294488051720.1089767994690.00674902237972-0.148646116681-0.0699221591832-0.05987338297280.004669788774430.003738527858210.03143950448050.13860161046-0.003330024063820.004547166618510.1539364463090.001545293000360.11723759653226.957580341-0.62299955898410.9603078075
52.083883553840.59953127119-0.503066918712.289124940890.4111934671782.01885481697-0.03263315503630.0486234955787-0.14137478775-0.0931664482026-0.01533138639140.02894869172830.230582621489-0.03767975695920.05141714943560.1394449039630.00480415575443-0.03779320130130.1169696480690.01159310833020.12062773356520.9266177005-19.885140998820.4537849462
62.1858318745-0.0331821913826-0.7446839096321.826175578410.4924065609511.783273867780.04699190488970.1257359471390.18483957851-0.3779133859310.0400625262711-0.0204180086248-0.2781011598460.123470953462-0.07829585744110.237899309494-0.0160833776901-0.009271269528140.1773089157560.004140064537980.20581528578314.28720989389.92915120102-24.8933471798
71.150074635880.521687770523-0.03420503493161.513514095080.677741556541.43366379074-0.0221429309826-0.087942003151-0.2134281257020.154776842201-0.0490700799190.09754520516750.245914685771-0.05599994750220.0713748384260.1469862255690.001185859688530.0006287380175320.1776772811230.01794683502610.2210055618759.28110256576-8.55675853564-12.479780897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 83 )
2X-RAY DIFFRACTION2chain 'A' and (resid 84 through 125 )
3X-RAY DIFFRACTION3chain 'A' and (resid 126 through 152 )
4X-RAY DIFFRACTION4chain 'A' and (resid 153 through 308 )
5X-RAY DIFFRACTION5chain 'A' and (resid 309 through 401 )
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 213 )
7X-RAY DIFFRACTION7chain 'B' and (resid 214 through 401 )

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