PDB-8g97: Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithin...

ID or keywords:

Entry

Database: PDB / ID: 8g97

Title

Adenylation domain structure from NRPS-like Delta-Poly-L-Ornithine synthetase (D-Ornithine bound)

Components

Dimodular nonribosomal peptide synthase

Keywords

LIGASE / Adenylation domain / NRPS / delta-poly-L-ornithine synthetase / nonribosomal peptide synthetase

Function / homology

Function and homology information

Ligases; Forming carbon-nitrogen bonds / amino acid activation for nonribosomal peptide biosynthetic process / secondary metabolite biosynthetic process / ligase activity / phosphopantetheine binding / plasma membrane / cytoplasm
Similarity search - Function

Biological species

Acinetobacter baumannii AB307-0294 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.51 Å

Authors

Patel, K.D. / Gulick, A.M.

Funding support

United States, 1items

Citation

Journal: Commun Biol / Year: 2023
Title: Structural and functional insights into delta-poly-L-ornithine polymer biosynthesis from Acinetobacter baumannii.
Authors: Patel, K.D. / Gulick, A.M.

History

Deposition	Feb 21, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 4, 2023	Provider: repository / Type: Initial release
Revision 1.1	May 1, 2024	Group: Database references / Category: citation Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8g97.cif.gz	394.2 KB	Display	PDBx/mmCIF format
PDB format	pdb8g97.ent.gz	270.5 KB	Display	PDB format
PDBx/mmJSON format	8g97.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8g97_validation.pdf.gz	885.2 KB	Display	wwPDB validaton report
Full document	8g97_full_validation.pdf.gz	899.1 KB	Display
Data in XML	8g97_validation.xml.gz	32.9 KB	Display
Data in CIF	8g97_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g9/8g97 ftp://data.pdbj.org/pub/pdb/validation_reports/g9/8g97	HTTPS FTP

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Related structure data

Related structure data	8g95SC 8g96C 8g98C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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) #90 - Jun 2007 Fatty Acid Synthase similarity (4) #165 - Sep 2013 Designed Protein Cages similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #49 - Jan 2004 Carbonic Anhydrase similarity (1)

Deposited unit

A: Dimodular nonribosomal peptide synthase

B: Dimodular nonribosomal peptide synthase

hetero molecules

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

1

A: Dimodular nonribosomal peptide synthase

hetero molecules

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

2

B: Dimodular nonribosomal peptide synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.837, 93.928, 152.257
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	1

NCS domain segments:

Ens-ID: 1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	THR	THR	TYR	TYR	(chain 'A' and (resid 8 through 340 or (resid 341...	A	A	8 - 171	10 - 173
1	2	LYS	LYS	ARG	ARG	(chain 'A' and (resid 8 through 340 or (resid 341...	A	A	178 - 410	180 - 412
2	3	THR	THR	TYR	TYR	(chain 'B' and (resid 8 through 47 or (resid 48...	B	B	8 - 171	10 - 173
2	4	LYS	LYS	ARG	ARG	(chain 'B' and (resid 8 through 47 or (resid 48...	B	B	178 - 410	180 - 412

#1: Protein	Dimodular nonribosomal peptide synthase Mass: 45944.387 Da / Num. of mol.: 2 / Fragment: residues 1-413 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii AB307-0294 (bacteria) Gene: dhbF_1, ABBFA_00818 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5K6CNB8
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical	ChemComp-ORD / D-ORNITHINE Type: D-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₁₂N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H₂O
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: 2.5 Å³/Da / Density % sol: 50.8 % / Description: Long rods
Crystal grow	Temperature: 293.15 K / Method: microbatch / pH: 7 / Details: 0.1 M Amm Bromide, 0.1 M BTP pH 7.0, 24% PEG 20K

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Data collection

Diffraction	Mean temperature: 110 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 20, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97946 Å / Relative weight: 1
Reflection	Resolution: 2.51→93.93 Å / Num. obs: 31440 / % possible obs: 98.26 % / Redundancy: 6.7 % / B_iso Wilson estimate: 59.6 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.0924 / R_pim(I) all: 0.03841 / Net I/σ(I): 15.04
Reflection shell	Resolution: 2.51→2.65 Å / Num. unique obs: 3069 / CC_1/2: 0.506

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
Coot	0.9.5	model building
AutoProcess		data reduction
PHASER		phasing
autoPROC		data reduction
Aimless		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 8G95

8g95

Resolution: 2.51→48.92 Å / SU ML: 0.3367 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.6413 / Stereochemistry target values: GeoStd + Monomer Library

	R_factor	Num. reflection	% reflection
R_free	0.2396	1994	6.36 %
R_work	0.1944	29380	-
obs	0.1972	31374	98.29 %

Solvent computation

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

Displacement parameters

B_iso mean: 74.62 Å²

Refinement step

Cycle: LAST / Resolution: 2.51→48.92 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6234	0	61	140	6435

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	6432
X-RAY DIFFRACTION	f_angle_d	0.6003	8757
X-RAY DIFFRACTION	f_chiral_restr	0.0452	1005
X-RAY DIFFRACTION	f_plane_restr	0.0042	1119
X-RAY DIFFRACTION	f_dihedral_angle_d	12.3538	3838

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 (%)
2.51-2.58	0.401	138	0.3456	2049	X-RAY DIFFRACTION	96.51
2.58-2.65	0.3507	142	0.3071	2064	X-RAY DIFFRACTION	99.06
2.65-2.72	0.3123	139	0.2938	2061	X-RAY DIFFRACTION	98.65
2.72-2.81	0.3375	140	0.2785	2067	X-RAY DIFFRACTION	98.09
2.81-2.91	0.3621	139	0.2749	2049	X-RAY DIFFRACTION	96.43
2.91-3.03	0.3491	140	0.2655	2074	X-RAY DIFFRACTION	99.15
3.03-3.17	0.3034	143	0.2317	2101	X-RAY DIFFRACTION	99.16
3.17-3.33	0.2955	142	0.2145	2102	X-RAY DIFFRACTION	99.07
3.33-3.54	0.2461	141	0.2002	2072	X-RAY DIFFRACTION	97.02
3.54-3.82	0.2093	143	0.1861	2091	X-RAY DIFFRACTION	99.16
3.82-4.2	0.2077	144	0.1535	2124	X-RAY DIFFRACTION	99.39
4.2-4.81	0.2038	141	0.1483	2100	X-RAY DIFFRACTION	97.14
4.81-6.06	0.1888	148	0.1681	2181	X-RAY DIFFRACTION	99.79
6.06-48.92	0.2065	154	0.1759	2245	X-RAY DIFFRACTION	97.52

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	2.92899281511	0.430263465108	1.11651390635	2.80453530323	-0.685002825619	6.58306050672	-0.494743297385	1.33400613972	0.0213405133951	-0.18639500149	0.540083354538	-0.11439440239	-0.0371963608195	0.288201198979	-0.0572117908626	0.48159787865	-0.00874167733688	0.00581516625559	0.527325725194	-0.0252392009849	0.412055253613	15.62411237	0.653837338651	-6.14543703632
2	2.08205921473	-0.840258108206	0.972276481851	2.69786957308	-1.24040299502	4.84380657041	-0.337836872302	0.36242115036	0.385641332012	0.165935119122	-0.0220104766437	-0.359298389562	-0.677383634708	0.935656899829	0.34313135888	0.518710127311	-0.17324495965	-0.117856196098	0.75251214204	0.0181434054387	0.581014460986	34.8285212675	5.17975589667	7.53028258598
3	2.98876121619	1.54772933988	1.14353667355	6.58131207982	0.383569054115	8.86237981211	-0.117980868449	-0.43887171943	-0.447677046765	0.804359578306	0.033360569624	-0.394880740813	0.474959691273	-0.0668242527542	0.0981171437149	0.605950017172	0.167036457438	0.00411029687289	0.66104367489	0.10031048273	0.629045234299	34.9100654029	-9.49928127138	16.1450745131
4	3.29835794208	0.0356923866382	1.03199434464	1.60457651687	-0.436920397153	4.30380739703	-0.19591737409	0.0314257212571	0.0710821167281	0.184268842875	0.0717896074484	-0.415956633743	-0.0357913723061	0.604360298765	0.101081540973	0.449166758525	-0.0307813134469	-0.0213415946634	0.496727269518	-0.0224792315104	0.464356047736	32.4549353103	-2.26476883703	7.14819068789
5	2.64123501847	-0.969662218973	0.145888706816	2.50905986322	0.0475346404653	6.65626082434	-0.324702045102	-0.096979953981	0.365943043189	0.503724610915	0.277139429639	-0.103593456175	-1.14981449334	-0.105333769093	0.114808441784	0.805757585192	0.0257524759038	-0.128990207204	0.469700948549	0.0223187512851	0.576033277468	21.0210414834	12.6521121222	12.7934103873
6	1.94857466938	-0.822030184014	-0.156296816481	1.59560292638	-0.435545360821	5.1289290619	-0.656440974727	-0.270989638197	0.379263149619	0.557479437152	0.391235421379	0.412371995288	-1.2464868835	-1.21523163075	0.185451827606	0.934788802473	0.341565561336	-0.0730233163099	0.667933771457	0.00444149910055	0.643772729748	8.87123753864	13.5358274066	16.3932889211
7	3.57658938896	-1.94553799814	0.448219774303	6.27880792985	0.235417066248	5.26565926852	-0.318047730854	-0.206098565064	0.0421647134453	0.127465208821	0.189141854539	0.376795126437	-0.771349039033	-0.74979373487	0.114618664584	0.597138577582	0.0820773270494	-0.0335962937935	0.619537850719	0.0301712169793	0.428281334637	7.88888435604	5.38126058587	8.71228644962
8	2.83752963811	-0.524131348159	1.14636650017	3.2623278159	-0.625643771021	5.2638297953	-0.12989908582	-0.22985944766	-0.172346968635	0.0428637796269	0.343583595391	0.559307275755	0.281424985807	-1.13007464638	-0.167070515191	0.399270124092	-0.0518341056366	0.0124128146238	0.84784693589	0.137033277247	0.588406030881	0.0878921964689	-6.86027415367	5.60642881267
9	4.24453430665	-1.5347328879	0.942623682466	2.96933160502	-0.439636724544	4.50025029435	-0.0831854938109	-0.334604716213	-0.688104760883	0.0451040848376	0.331548530624	0.161987548744	0.599274431592	-0.539401861491	-0.222494441732	0.615207456473	-0.13456249169	-0.00433955827261	0.660865562269	0.0812604510757	0.661530186691	8.22282161268	-13.203293383	4.95562162727
10	1.59061365437	-0.52296243386	0.605703758042	2.34888888695	0.241659503503	4.10533252873	0.0888229649581	0.137546565444	0.178006517174	-0.276993520043	-0.29005598554	-0.00316266656802	-0.423849877719	-0.266312986375	0.206347331795	0.597139491866	0.133843747008	-0.00708569291016	0.589040695587	0.0498571091008	0.447697610865	8.95072623271	13.1159555747	-33.2799610584
11	2.96110337858	-0.795688172425	0.397120345229	2.94600091466	-0.0874469510802	7.52977925969	-0.136866109936	0.0976986350282	0.428954477921	0.238467081296	-0.143663681774	-0.199453531018	-1.06697672247	0.477413095998	0.271562785571	0.692711397501	-0.0807621964571	-0.0186120087135	0.530058340662	0.0473789193274	0.639315403941	17.8766049341	20.3704199537	-24.1216635379
12	2.72285630525	-0.457841470302	0.339562856004	1.54378924084	-0.748828621824	4.34448877203	0.272466542146	0.00288263772637	-0.151941861449	-0.228394664222	-0.196643376599	0.0356040473493	0.630890675115	-0.136383524	-0.0664911541067	0.49515576114	0.0252433106436	-0.048192254468	0.493996590363	-0.0215835089326	0.411001514409	10.3165131077	-4.01766933591	-28.0541783199
13	1.82279905781	0.581963859339	-0.0561897539165	4.93879278958	-3.02356047494	6.77792155071	-0.025729921219	0.0463616981557	-0.183933691326	-0.488163199904	-0.0356360124887	-0.543106048065	1.65409257021	0.944403524934	0.0727264442747	1.10303041793	0.458530848926	0.016134492845	0.859915265732	-0.0219310321212	0.599681765681	25.5960234619	-12.2249660258	-34.686429243

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 7 through 36 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 37 through 109 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 110 through 128 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 129 through 200 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201 through 254 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 255 through 294 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 295 through 318 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 319 through 352 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 353 through 411 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 8 through 109 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 110 through 180 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 181 through 378 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 379 through 411 )

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