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

ID or keywords:

Entry

Database: PDB / ID: 6vhw

Title

Klebsiella oxytoca NpsA N-terminal subdomain in complex with 3-hydroxybenzoyl-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: 1.83 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	6vhw.cif.gz	354.8 KB	Display	PDBx/mmCIF format
PDB format	pdb6vhw.ent.gz	255.5 KB	Display	PDB format
PDBx/mmJSON format	6vhw.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6vhw_validation.pdf.gz	430.2 KB	Display	wwPDB validaton report
Full document	6vhw_full_validation.pdf.gz	433.4 KB	Display
Data in XML	6vhw_validation.xml.gz	2.5 KB	Display
Data in CIF	6vhw_validation.cif.gz	11.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vh/6vhw ftp://data.pdbj.org/pub/pdb/validation_reports/vh/6vhw	HTTPS FTP

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Related structure data

Related structure data	6vhtC 6vhuSC 6vhvC 6vhxC 6vhyC 6vhzC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3rv7-1 4k6n-d 3qm0-d 5l7l-d 6c3i-2 6cg2-1 6vhx-1 6wf2-1 2q8k-d 2i6y-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

89.8 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
45.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: NpsA Adenylation Domain

hetero molecules

defined by author
44.7 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)	77.436, 60.284, 80.253
Angle α, β, γ (deg.)	90.000, 101.009, 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 , 7 types, 262 molecules

#2: Chemical	ChemComp-R2V / 5'-deoxy-5'-{[(3-hydroxybenzene-1-carbonyl)sulfamoyl]amino}adenosine Mass: 465.440 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₁₉N₇O₇S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: 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
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Chemical	ChemComp-BR / BROMIDE ION Mass: 79.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Br
#7: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 249 / 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: 2.15 Å³/Da / Density % sol: 42.89 % / 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: 7.5-8.0

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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 24, 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: 1.83→78.78 Å / Num. obs: 60901 / % possible obs: 95.2 % / Redundancy: 6.7 % / B_iso Wilson estimate: 31.8 Å² / CC_1/2: 0.998 / R_pim(I) all: 0.039 / R_rim(I) all: 0.103 / R_sym value: 0.095 / Net I/σ(I): 10.8
Reflection shell	Resolution: 1.83→1.87 Å / Redundancy: 6.8 % / Num. unique obs: 3129 / CC_1/2: 0.32 / R_pim(I) all: 0.89 / R_rim(I) all: 2.354 / R_sym value: 2.177 / % possible all: 98.5

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6vhu

6vhu

Resolution: 1.83→78.78 Å / SU ML: 0.269 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.4446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2312	2889	4.74 %
R_work	0.2011	58011	-
obs	0.2025	60900	95.2 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 41.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.83→78.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5874	0	109	249	6232

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0072	6131
X-RAY DIFFRACTION	f_angle_d	0.9132	8369
X-RAY DIFFRACTION	f_chiral_restr	0.0582	989
X-RAY DIFFRACTION	f_plane_restr	0.0065	1072
X-RAY DIFFRACTION	f_dihedral_angle_d	13.4189	3658

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 (%)
1.83-1.86	0.3772	167	0.338	2831	X-RAY DIFFRACTION	98.52
1.86-1.9	0.3713	147	0.3158	2832	X-RAY DIFFRACTION	98.61
1.9-1.93	0.3667	137	0.3034	2852	X-RAY DIFFRACTION	98.48
1.93-1.97	0.3033	152	0.2824	2826	X-RAY DIFFRACTION	98.58
1.97-2.01	0.3046	136	0.2754	2867	X-RAY DIFFRACTION	98.62
2.01-2.05	0.2744	117	0.2592	2856	X-RAY DIFFRACTION	99.1
2.05-2.1	0.3265	67	0.2656	1414	X-RAY DIFFRACTION	49.15
2.1-2.15	0.2897	139	0.2391	2867	X-RAY DIFFRACTION	99.04
2.15-2.21	0.2384	149	0.2355	2844	X-RAY DIFFRACTION	99.07
2.21-2.27	0.2561	90	0.2305	1893	X-RAY DIFFRACTION	64.63
2.27-2.35	0.2472	127	0.2247	2897	X-RAY DIFFRACTION	99.31
2.35-2.43	0.278	143	0.2229	2860	X-RAY DIFFRACTION	99.27
2.43-2.53	0.233	141	0.2185	2868	X-RAY DIFFRACTION	99.5
2.53-2.64	0.2522	126	0.2218	2899	X-RAY DIFFRACTION	99.44
2.64-2.78	0.2573	149	0.2259	2894	X-RAY DIFFRACTION	99.57
2.78-2.96	0.2848	129	0.2147	2911	X-RAY DIFFRACTION	99.61
2.96-3.19	0.244	169	0.21	2871	X-RAY DIFFRACTION	99.77
3.19-3.51	0.222	180	0.1899	2865	X-RAY DIFFRACTION	99.54
3.51-4.01	0.1773	116	0.1687	2956	X-RAY DIFFRACTION	99.81
4.01-5.06	0.1771	139	0.1481	2939	X-RAY DIFFRACTION	99.77
5.06-78.78	0.1962	169	0.1775	2969	X-RAY DIFFRACTION	99.49

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	1.97059578011	-3.36300768835	2.10835050328	6.21979494038	-4.02016087297	2.86151671618	0.0770922155745	-0.123056188799	-0.193597299302	-0.0157802584001	-0.0638542720072	-0.14579326687	0.240037109684	0.287652491917	0.0330703504643	0.242057808092	-0.0469291348888	-0.0271344262076	0.422316659686	-0.0861577865421	0.317555200228	40.5500360387	-1.02431487194	30.7134122338
2	4.73549242135	0.620052192621	-1.29583096636	2.0989870329	0.198009580094	2.7753093994	0.0773847633906	0.0279261887245	0.240027045225	0.004436176759	0.0169133155527	0.21685372968	-0.262395266243	-0.0475234934011	-0.100558037439	0.249996471529	-0.00800203271021	0.0144056084577	0.159356652855	0.00589062493741	0.208803224838	24.0127030397	13.010252498	24.9926807378
3	2.79450917913	-3.07484148695	3.06808088495	8.20302190964	-4.64337226786	5.18536649962	0.0110149271987	0.00804285846069	0.462458093016	0.294526345576	-0.362307124344	-0.678871721632	-0.755987044035	0.342097724265	0.35664355738	0.433390158149	-0.110515639335	0.0724594477052	0.392916282847	-0.0522580114223	0.273234140345	27.7996967476	15.7120859339	33.7063442517
4	1.12028007036	-0.0105259770958	-0.774004143931	1.21741871887	-0.210081075695	2.93619020926	0.0703336215544	0.154333693533	-0.0111527078265	-0.12341381409	-0.0268831287372	0.000808804568006	0.129746912414	0.124380636131	-0.0390606241041	0.191219538846	0.0137508359765	-0.0206330970975	0.244491235052	-0.0117764801409	0.206367625968	28.9120086446	-1.24673098636	11.0340914442
5	3.26260370244	1.30790110065	-2.10861822003	5.44458298945	-1.67027400005	2.31827781824	0.0201875780533	0.619990734912	-0.680056378035	-0.440984266368	0.117048175511	-0.327874586009	0.54318255812	-0.03628771482	-0.0597373942562	0.278689671099	0.0508671688431	-0.0288451353728	0.386967269919	-0.0889142586983	0.299005966741	29.4463602472	-17.2486929645	12.8523734909
6	1.39377217795	-0.828654571934	-0.0723148242761	6.27475720556	1.18100506497	5.6325727228	0.112008393435	0.248985054875	-0.330278535438	-0.0285675390708	-0.118765233018	0.184195206437	0.650128688692	0.0283650280744	0.0120106175564	0.278817395408	-0.0143480101738	-0.0703974394291	0.24222639182	0.0222226260737	0.275087565379	20.8136946125	-20.0311684093	22.3256505731
7	4.60911779705	0.472544691821	-1.44894462855	2.83818928321	0.117876384037	3.19938759265	0.00422936612429	0.222045131738	0.153438324187	-0.665059645371	0.0946236604382	0.130280409931	0.047843093481	0.202463217772	-0.0962945227552	0.47931197335	-0.00303492367911	0.0255605692387	0.214754116268	0.048626364633	0.348861157189	19.1999815783	13.8342617178	-25.5105096613
8	6.55770720096	5.65944730414	3.6714479776	6.88903933232	4.1991539167	2.85565882444	-0.172859695264	0.0540590004514	1.1507794375	-1.15850213525	-0.330893619594	0.919343675555	0.141745280508	-0.245285605616	0.494628550403	0.742420814911	0.0432143248879	-0.000555386393395	0.426644370893	0.105158203257	0.50553347724	19.861934527	17.8787138374	-32.9954501499
9	1.30895113302	0.52007851543	-0.0257928013006	3.61669118696	-0.318061728458	1.97522173846	0.0894124572591	-0.102701427759	0.191081309196	-0.18552731909	-0.0337120958552	0.34993753161	0.0720250594812	-0.0160414791828	-0.0551584978432	0.223118883138	0.0190118233538	0.0102336372618	0.167619010621	-0.00880379676929	0.309091888075	11.5066716429	4.2963306641	-9.84794851017
10	2.04718814671	0.685396857789	-0.776481882448	5.11707305682	1.85599853389	2.48800206868	-0.130733176184	-0.0950804917708	-0.302061470758	-0.182159528328	-0.139248856259	0.100365094617	0.433551369262	0.0437090284983	0.250867497324	0.593469378462	0.0389688071699	-0.00532491468139	0.2466265045	0.0247868731033	0.377544328775	7.5710665087	-14.4527902887	-17.4805635752

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 125 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 126 through 152 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 153 through 308 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 309 through 335 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 336 through 402 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 10 through 125 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 126 through 152 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 153 through 296 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 297 through 403 )

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