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- PDB-6vhz: Klebsiella oxytoca NpsA N-terminal subdomain in complex with anth... -

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Basic information

Entry
Database: PDB / ID: 6vhz
TitleKlebsiella oxytoca NpsA N-terminal subdomain in complex with anthranilyl-AMSN
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 / Chem-QXP / Thioester reductase
Similarity search - Component
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 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)89,18711
Polymers87,9212
Non-polymers1,2669
Water1,33374
1
A: NpsA Adenylation Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5315
Polymers43,9601
Non-polymers5714
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NpsA Adenylation Domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,6566
Polymers43,9601
Non-polymers6955
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-63 kcal/mol
Surface area30490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.013, 61.408, 80.518
Angle α, β, γ (deg.)90.000, 100.434, 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

#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
#2: Chemical ChemComp-QXP / 5'-{[(benzenecarbonyl)sulfamoyl]amino}-5'-deoxyadenosine


Mass: 464.456 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N8O6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.13 Å3/Da / Density % sol: 42.25 % / 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: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.12→79.19 Å / Num. obs: 38904 / % possible obs: 92.1 % / Redundancy: 6.7 % / Biso Wilson estimate: 45.91 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.023 / Rrim(I) all: 0.06 / Rsym value: 0.055 / Net I/σ(I): 17.5
Reflection shellResolution: 2.12→2.16 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2036 / CC1/2: 0.852 / Rpim(I) all: 0.332 / Rrim(I) all: 0.861 / Rsym value: 0.792 / % possible all: 97.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
autoPROC1.0.5 (20190301)data scaling
PHASERphasing
Cootmodel building
PHENIX1.15_3459refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vhu

6vhu


Resolution: 2.12→50.37 Å / SU ML: 0.2859 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.1405
RfactorNum. reflection% reflection
Rfree0.2273 1853 4.77 %
Rwork0.2027 --
obs0.2039 38876 92.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.79 Å2
Refinement stepCycle: LAST / Resolution: 2.12→50.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5632 0 62 74 5768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00695798
X-RAY DIFFRACTIONf_angle_d0.81137922
X-RAY DIFFRACTIONf_chiral_restr0.0599957
X-RAY DIFFRACTIONf_plane_restr0.00441011
X-RAY DIFFRACTIONf_dihedral_angle_d16.00612027
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.180.33951650.28772954X-RAY DIFFRACTION97.29
2.18-2.240.30781250.27232718X-RAY DIFFRACTION98.2
2.24-2.310.3042940.24641878X-RAY DIFFRACTION99
2.31-2.40.26251520.24513074X-RAY DIFFRACTION99.35
2.4-2.490.28321740.23673028X-RAY DIFFRACTION99.38
2.49-2.610.2711560.23633060X-RAY DIFFRACTION99.17
2.61-2.740.2861380.24152558X-RAY DIFFRACTION83.13
2.74-2.910.34291660.24843005X-RAY DIFFRACTION97.9
2.91-3.140.29831280.24373095X-RAY DIFFRACTION99.75
3.14-3.460.27931100.2242852X-RAY DIFFRACTION99.26
3.46-3.960.21121050.19482581X-RAY DIFFRACTION82.93
3.96-4.980.16331640.15713067X-RAY DIFFRACTION98.51
4.98-50.370.18391760.17453153X-RAY DIFFRACTION98.84
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)
12.96537131801-0.355590561195-0.2854472856811.73057972986-0.7815320685772.20651416087-0.139704396381-0.7941538299721.086346196420.7388125571870.139511726956-1.28249738699-0.6803272441680.386989888215-0.07604037789070.60384190705-0.0370025884494-0.1510007952050.582635473948-0.240577324110.99626718248529.335347781623.234617954925.1798895016
23.40267696142-2.23605172086-0.9212883633184.103016671270.1594030207143.01416768818-0.231587825027-0.5576195787550.3667780225420.5370239274960.201348410102-0.21094006718-0.103253322357-0.5556288805760.06998970695550.4452828867690.0348746433359-0.03152822951690.532950721618-0.1266478187610.39333406719414.364162964816.095142981227.3202777585
33.40687379338-1.63019288971-1.099909999771.47922105698-0.6683856329412.50144521517-0.0515800512238-0.440853021368-0.760044342307-0.03431922960030.04999699601950.1696701818180.64705014869-0.222543300779-0.03907498499020.612140452107-0.0187240867669-0.1376595830220.476076934496-0.03252289126940.5541580955320.97638008851.9117942693924.3506135529
42.51410693748-1.292971053410.6016279306752.356248529811.112783993344.580340202490.2093684497310.2156981354540.378553556216-0.226823828621-0.0340588926385-0.6631739343470.05766198843440.355926499232-0.1456407648670.322427040362-0.01097433133910.08240244353180.3452841709030.02484694799390.53738671982828.70269627110.16547441316.96734721201
52.09544718754-0.210788106716-0.03981085131262.718590608381.004078602413.278465161070.1164398881370.26238813992-0.5453995424540.04708227641250.247390472733-0.6667839708691.032383947820.503907869971-0.3915248028130.6492285468360.103958826339-0.06498591169940.531602986588-0.1066580588940.61756850409432.7409130351-2.6335285268811.3148566799
62.282121516570.431794307887-0.4224458817173.018130808240.5091872623112.48499695461-0.02164228648170.129979757475-0.807016671140.7439853858860.275708426801-0.07164495119911.10386229074-0.132347443458-0.2876107222951.083375666440.0112894168489-0.2451727145180.5866934188690.07293564451040.61589882326825.1339572312-10.508898677525.9815728737
71.98286890914-0.2638231190990.1287201177991.520342276940.2697231397563.526320862480.2031707733840.433598557217-0.4711530763370.344994020285-0.117497332259-0.9922404480671.207252598881.11368182524-0.1691878631681.164513581910.230838023004-0.3030421024330.840119941324-0.008024660724620.82149003825830.5198243511-11.674624167118.2401933177
82.150302492521.03417209517-0.2275941384722.60562633553-0.2811288363265.032044565960.007139988285960.01922118909660.146513337549-0.08747941933690.113249235657-0.0271672429261-0.670960122786-0.190133826205-0.1031981513670.3541038227980.1059138473920.01630083100840.2912362999530.03423848808410.28115980799511.886490386113.9963958186-27.4177368837
90.7043047376650.5329213240710.4183531387041.33488682317-0.1406168071393.80020921270.0818781587167-0.3616415747370.0335524373380.2108076351350.006747696631070.0722149465977-0.213254571443-0.501469616389-0.09040235063250.3058778156970.07721516944730.05471331539610.5021036737880.03942677460240.3288858854237.045862873976.83568505964-8.56151920065
100.9594977380210.5490139023140.4753319322031.29734716210.7580926784642.801036803510.173216659769-0.543749245811-0.2570333808630.313926638340.137804616727-0.105449850260.759403320189-0.208308650461-0.2956344452140.43442200164-0.0290920474237-0.00667317277810.5107777027010.1396315072220.3948981927058.52566490042-6.9653176698-7.22571621708
111.58029095245-1.332109200460.118710414014.43649133218-0.3331128241172.38074406136-0.168624991903-0.261854136742-0.3952861208330.3501091582630.132409937221-0.2661190226640.556275007695-0.1746187229740.05228369595340.5987120755710.012492060501-0.07011864612260.330725044017-0.009602755498820.46359208790117.0197275718-16.4363548293-22.3771361739
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 56 )
2X-RAY DIFFRACTION2chain 'A' and (resid 57 through 159 )
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 180 )
4X-RAY DIFFRACTION4chain 'A' and (resid 181 through 296 )
5X-RAY DIFFRACTION5chain 'A' and (resid 297 through 329 )
6X-RAY DIFFRACTION6chain 'A' and (resid 330 through 376 )
7X-RAY DIFFRACTION7chain 'A' and (resid 377 through 402 )
8X-RAY DIFFRACTION8chain 'B' and (resid 3 through 180 )
9X-RAY DIFFRACTION9chain 'B' and (resid 181 through 276 )
10X-RAY DIFFRACTION10chain 'B' and (resid 277 through 329 )
11X-RAY DIFFRACTION11chain 'B' and (resid 330 through 401 )

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