PDB-6vhx: Klebsiella oxytoca NpsA N-terminal subdomain in complex with 3-hy...

ID or keywords:

Entry

Database: PDB / ID: 6vhx

Title

Klebsiella oxytoca NpsA N-terminal subdomain in complex with 3-hydroxyanthranilyl-AMSN

Components

NpsA Adenylation Domain

Keywords

BIOSYNTHETIC PROTEIN / adenylation / tilivalline / tilimycin / NRPS / nonribosomal peptide synthetase

Function / homology

Function and homology information

ligase activity
Similarity search - Function

Biological species

Klebsiella oxytoca (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 Å

Authors

Kreitler, D.F. / Gulick, A.M.

Funding support

United States, 1items

Citation

Journal: 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

Deposition	Jan 10, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2020	Provider: repository / Type: Initial release
Revision 1.1	Jul 22, 2020	Group: 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 1.2	Oct 11, 2023	Group: 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6vhx.cif.gz	354.4 KB	Display	PDBx/mmCIF format
PDB format	pdb6vhx.ent.gz	254.1 KB	Display	PDB format
PDBx/mmJSON format	6vhx.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vhx_validation.pdf.gz	429.9 KB	Display	wwPDB validaton report
Full document	6vhx_full_validation.pdf.gz	432.7 KB	Display
Data in XML	6vhx_validation.xml.gz	2.2 KB	Display
Data in CIF	6vhx_validation.cif.gz	11.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vh/6vhx ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vhx	HTTPS FTP

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Related structure data

Related structure data	6vhtC 6vhuC 6vhvC 6vhwSC 6vhyC 6vhzC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6c3i-2 3rv7-4 7lqx-d 4rnv-4 4wiw-6 5znt-d 6c3i-1 5l7l-d 6mev-2 1ceo-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#78 - Jun 2006 Luciferase similarity (6) #122 - Feb 2010 Enhanceosome similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: NpsA Adenylation Domain

B: NpsA Adenylation Domain

hetero molecules

89.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NpsA Adenylation Domain

hetero molecules

defined by author
Evidence: gel filtration
44.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NpsA Adenylation Domain

hetero molecules

defined by author
44.8 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	77.073, 60.233, 79.960
Angle α, β, γ (deg.)	90.000, 101.550, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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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

#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 , 6 types, 297 molecules

#2: Chemical	ChemComp-QXG / 5'-{[(2-amino-3-hydroxybenzene-1-carbonyl)sulfamoyl]amino}-5'-deoxyadenosine Mass: 480.455 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₀N₈O₇S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#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: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.07 Å³/Da / Density % sol: 40.53 % / Description: 3D
Crystal grow	Temperature: 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

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03322 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 25, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03322 Å / Relative weight: 1
Reflection	Resolution: 1.7→60.79 Å / Num. obs: 73338 / % possible obs: 92.9 % / Redundancy: 6.6 % / B_iso Wilson estimate: 25.07 Å² / CC_1/2: 0.999 / R_pim(I) all: 0.039 / R_rim(I) all: 0.101 / R_sym value: 0.093 / Net I/σ(I): 11.9
Reflection shell	Resolution: 1.7→1.73 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 0.8 / Num. unique obs: 3912 / CC_1/2: 0.366 / R_pim(I) all: 0.9 / R_rim(I) all: 2.322 / R_sym value: 2.137 / % possible all: 100

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Processing

Software

Name	Version	Classification
XDS		data reduction
Aimless	0.7.4	data scaling
autoPROC	1.0.5 (20181127)	data scaling
PHASER		phasing
Coot		model building
PHENIX	1.15_3459	refinement

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6vhw

6vhw

Resolution: 1.7→60.79 Å / SU ML: 0.2219 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.746

	R_factor	Num. reflection	% reflection
R_free	0.2174	3492	4.76 %
R_work	0.1913	-	-
obs	0.1925	73315	92.85 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 34.13 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→60.79 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5885	0	94	287	6266

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	6125
X-RAY DIFFRACTION	f_angle_d	0.9326	8355
X-RAY DIFFRACTION	f_chiral_restr	0.059	980
X-RAY DIFFRACTION	f_plane_restr	0.0061	1072
X-RAY DIFFRACTION	f_dihedral_angle_d	17.965	2208

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.7-1.72	0.3636	151	0.3309	2978	X-RAY DIFFRACTION	99.74
1.72-1.75	0.3101	158	0.3026	2982	X-RAY DIFFRACTION	99.97
1.75-1.78	0.2879	164	0.2905	2976	X-RAY DIFFRACTION	99.94
1.78-1.8	0.3284	155	0.2745	2948	X-RAY DIFFRACTION	99.97
1.8-1.83	0.284	144	0.2622	3032	X-RAY DIFFRACTION	100
1.83-1.86	0.2583	148	0.2505	2959	X-RAY DIFFRACTION	100
1.86-1.9	0.2869	154	0.2345	2990	X-RAY DIFFRACTION	99.97
1.9-1.93	0.2735	153	0.2396	3005	X-RAY DIFFRACTION	99.87
1.93-1.97	0.2464	151	0.22	2986	X-RAY DIFFRACTION	99.97
1.97-2.02	0.2558	171	0.2122	2961	X-RAY DIFFRACTION	99.94
2.02-2.06	0.2611	125	0.2114	2207	X-RAY DIFFRACTION	98.6
2.06-2.12	0.2705	63	0.2206	1018	X-RAY DIFFRACTION	97.56
2.12-2.17	0.2198	127	0.1959	3023	X-RAY DIFFRACTION	99.97
2.17-2.24	0.2651	135	0.1882	2996	X-RAY DIFFRACTION	99.9
2.24-2.31	0.2066	90	0.193	2041	X-RAY DIFFRACTION	67.48
2.31-2.39	0.2347	130	0.1886	3023	X-RAY DIFFRACTION	99.9
2.39-2.49	0.1849	126	0.1777	3021	X-RAY DIFFRACTION	99.94
2.49-2.6	0.2116	149	0.1879	3013	X-RAY DIFFRACTION	100
2.6-2.74	0.2417	108	0.2038	2265	X-RAY DIFFRACTION	75.09
2.74-2.91	0.2434	153	0.1934	3003	X-RAY DIFFRACTION	99.97
2.91-3.13	0.2005	174	0.1945	3020	X-RAY DIFFRACTION	99.97
3.13-3.45	0.2219	128	0.1816	2685	X-RAY DIFFRACTION	99.5
3.45-3.95	0.209	119	0.1629	2521	X-RAY DIFFRACTION	87.45
3.95-4.97	0.1635	143	0.1533	3061	X-RAY DIFFRACTION	99.88
4.97-60.79	0.1795	173	0.1814	3109	X-RAY DIFFRACTION	99.91

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	1.0892249257	-2.79550482466	0.873831608304	7.94360410686	-3.16840859107	1.57867189632	-0.145238055566	-0.0788814402296	-0.111149906662	0.329806812093	0.0632128104577	-0.230441882479	0.127930711976	0.378186466032	0.12909093477	0.292254975122	0.0268065708987	0.00280302182989	0.434907893568	-0.0510791094621	0.279761951029	40.288723611	-0.868702494959	30.6112454728
2	4.17711667882	0.574265528555	-1.822406578	1.77760879013	0.0044043390342	2.83939568045	0.058615871406	-0.190243939067	0.205469317761	0.100810074921	0.0374914253797	-0.0441399566126	-0.197414226498	0.360186777864	-0.118160108738	0.212132138712	-0.0242648593155	-0.00792848834682	0.193041213696	-0.0133584519155	0.137678538354	31.0580788619	13.926714597	25.6061655227
3	5.12539039822	1.79256172815	1.23294454	3.63615836198	1.59550505224	2.95981142647	0.00768352863287	0.0467668583922	0.415702056675	-0.28780433019	-0.0319458185238	0.688391331492	-0.424121474035	-0.322594351064	0.0214083740394	0.267870224282	0.0528942626907	-0.0210709436497	0.203667458605	0.012377469068	0.24589070618	12.2468676651	11.6139801755	23.936729022
4	2.47552127543	-2.94045835986	2.51100669987	8.12663794714	-4.40139235281	4.39272935714	-0.205705712811	-0.0286625423166	0.454559681578	0.370787665607	-0.231212987247	-0.818705098264	-0.614537789865	0.326976783466	0.411048794138	0.367430497221	-0.0287269098345	0.0178487283432	0.286642463987	-0.0534172451193	0.182244206474	26.7884894569	15.8995593306	33.2219151675
5	0.627388153158	-0.179638567548	-0.667796512233	1.12513084764	0.0245487588674	2.82961691871	0.0268662914114	0.125098479449	-0.0283898431389	-0.0911158813699	-0.0502886247711	-0.0246130088842	0.039371429372	0.144052455452	0.0147270069118	0.190430664802	0.013481948614	-0.0019888236994	0.212322471763	-0.00123430678739	0.155622291366	28.7436278636	0.972388625402	11.9662212574
6	0.921838024472	0.0542551758862	-1.48668899863	1.32009621645	-1.17542093753	6.22465047672	0.057470050086	0.334465099124	-0.242257349937	-0.327894946636	-0.0854979278682	-0.136239884567	0.529611076208	0.195130992696	0.0602243865237	0.314586290851	0.0694576987892	0.00342031189124	0.275754672091	-0.0573099314351	0.177504077111	29.9142604182	-11.0568528299	7.51429520386
7	4.15704489267	-0.937986707781	-0.496030043403	6.03025913115	1.22098621095	3.95706915637	0.166483163127	0.351320305894	-0.667565789322	-0.253953586438	-0.0726902275698	0.256651870413	0.655239565467	-0.0716750050834	-0.0469569855699	0.416180018532	0.0225941357917	-0.0925305058545	0.212180929329	0.0213795598968	0.257095757885	20.5815857583	-20.7014750992	21.805150185
8	2.35475933116	-0.444195076202	0.960208427342	4.66374141133	-0.339261205262	6.3449493683	0.263380056397	0.27582304129	-0.314817140226	-0.277911175431	-0.108017839227	0.170218804729	0.378040850261	0.310068621521	-0.108803906825	0.322590628532	-0.00496776606643	-0.0612233987495	0.21552730119	0.0212216091119	0.275072621456	21.0912939014	-19.8711379317	21.8296351207
9	4.00451376576	-0.510756290933	-0.970290980533	2.11151706624	0.749321358666	1.9091991627	0.0820238902246	0.121265031455	0.199167624885	-0.408679053039	0.0733529626897	-0.0909977786815	-0.152091428104	0.0819166943418	-0.147383864623	0.381687178059	-0.0247768226804	0.0676210929399	0.149211689687	0.0485285895766	0.310089674395	18.6567318712	14.1300031311	-25.0358163875
10	1.09805406206	-0.0249456189438	-0.392170920277	1.62459977429	0.339817063218	1.40667620041	0.0148804491003	-0.0627037106611	0.196144765174	-0.141764009351	-0.0113938395685	0.00660791632508	-0.0623513281911	0.0114558589138	-0.000778001825466	0.175405474929	0.011067797217	0.0181603577994	0.125094376645	-0.00580136907849	0.20415697004	13.0236920005	6.58364720725	-13.7691671617
11	1.70634918104	0.417524837962	-0.802316543239	3.92689699593	0.805377272838	2.6906416611	-0.0442065782085	-0.142312260857	-0.229119533671	0.109542727272	-0.0177555723175	-0.0454384023273	0.316281067605	-0.00762630520626	0.0780346613313	0.213520022894	0.0143983976942	-0.0190205563787	0.154720891743	0.0104623248289	0.213505889857	7.65854297418	-14.4749695454	-17.5841928787

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 84 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 85 through 125 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 152 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 153 through 276 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 277 through 329 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 330 through 363 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 364 through 401 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 10 through 118 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 124 through 296 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 297 through 403 )

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