PDB-7ug3: Crystal structure of adenosylmethionie-8-amino-7-oxononanoate ami...

ID or keywords:

Entry

Database: PDB / ID: 7ug3

Title

Crystal structure of adenosylmethionie-8-amino-7-oxononanoate aminotransferase from Klebsiella pneumoniae

Components

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

Keywords

TRANSFERASE /

Structural Genomics / NIAID / ESKAPEE /

Pathogen / Seattle Structural Genomics Center for Infectious Disease / SSGCID

Function / homology

Function and homology information

adenosylmethionine-8-amino-7-oxononanoate transaminase /

adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process /

pyridoxal phosphate binding /

cytoplasm
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of adenosylmethionie-8-amino-7-oxononanoate aminotransferase from Klebsiella pneumoniae
Authors: Yang, M. / Edwards, T.E. / Horanyi, P.S. / Lorimer, D.D.

History

Deposition	Mar 23, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7ug3.cif.gz	759.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7ug3.ent.gz	524.9 KB	Display	PDB format
PDBx/mmJSON format	7ug3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ug/7ug3 ftp://data.pdbj.org/pub/pdb/validation_reports/ug/7ug3	HTTPS FTP

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Related structure data

Related structure data	1qj5S S: Starting model for refinement
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: Klpnc.01026.b

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

C: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

D: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

hetero molecules

193 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

B: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

hetero molecules

defined by author&software
Evidence: gel filtration
96.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

D: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

hetero molecules

defined by author&software
96.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	85.070, 90.830, 103.860
Angle α, β, γ (deg.)	90.000, 93.874, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb

#1: Protein	Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / 7 / 8-diamino-pelargonic acid aminotransferase / DAPA AT / DAPA aminotransferase / 8- ...7 / 8-diamino-pelargonic acid aminotransferase / DAPA AT / DAPA aminotransferase / 8-diaminononanoate synthase / DANS / Diaminopelargonic acid synthase Mass: 48317.488 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Gene: bioA, B4U61_18450, B5L96_06770, SAMEA4873619_00999 / Production host: Escherichia coli (E. coli) References: UniProt: A0A422Z2E3, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 941 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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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: 40.65 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.1 Details: KlpnC.01026.b.B1.PW39017 at 37 mg/mL with 5 mM SAH against JCSG+ screen condition C4: 0.1 M Hepes pH 7.1, 10% PEG 6000, supplemented with 25% ethylene glycol as cryo-protectant, crystal ...Details: KlpnC.01026.b.B1.PW39017 at 37 mg/mL with 5 mM SAH against JCSG+ screen condition C4: 0.1 M Hepes pH 7.1, 10% PEG 6000, supplemented with 25% ethylene glycol as cryo-protectant, crystal tracking ID 322320c4, unique puck ID twl7-9, APS 21 ID-F 11/04/21

Crystal

Density Matthews: 2.07 Å³/Da / Density % sol: 40.65 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: KlpnC.01026.b.B1.PW39017 at 37 mg/mL with 5 mM SAH against JCSG+ screen condition C4: 0.1 M Hepes pH 7.1, 10% PEG 6000, supplemented with 25% ethylene glycol as cryo-protectant, crystal ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.9787 Å

Detector

Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 4, 2021

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9787 Å / Relative weight: 1

Reflection

Resolution: 1.9→50 Å / Num. obs: 123933 / % possible obs: 99.8 % / Redundancy: 4.129 % / B_iso Wilson estimate: 35.725 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.047 / R_rim(I) all: 0.054 / Χ²: 0.938 / Net I/σ(I): 17.89

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.9-1.95	3.443	0.481	2.5	9069	0.789	0.572	98.8
1.95-2	4.05	0.431	3.24	8895	0.861	0.498	100
2-2.06	4.206	0.326	4.42	8674	0.924	0.374	99.9
2.06-2.12	4.215	0.246	5.86	8416	0.95	0.282	100
2.12-2.19	4.217	0.19	7.4	8132	0.974	0.218	99.9
2.19-2.27	4.22	0.151	9.06	7941	0.983	0.173	100
2.27-2.36	4.226	0.121	11.18	7622	0.988	0.139	99.9
2.36-2.45	4.233	0.106	12.59	7319	0.99	0.121	99.9
2.45-2.56	4.228	0.089	14.72	7014	0.993	0.103	99.9
2.56-2.69	4.228	0.074	17.34	6746	0.995	0.085	99.8
2.69-2.83	4.224	0.058	21.77	6447	0.997	0.066	100
2.83-3	4.211	0.048	25.46	6027	0.997	0.055	99.9
3-3.21	4.192	0.04	29.93	5703	0.998	0.046	99.8
3.21-3.47	4.169	0.034	35.02	5313	0.998	0.039	99.8
3.47-3.8	4.165	0.03	39.34	4901	0.999	0.034	99.9
3.8-4.25	4.14	0.027	42.95	4430	0.999	0.03	99.8
4.25-4.91	4.117	0.025	45.45	3913	0.999	0.029	99.8
4.91-6.01	4.105	0.025	44.53	3353	0.999	0.029	100
6.01-8.5	4.052	0.023	45.71	2593	0.999	0.027	100
8.5-50	3.856	0.022	48.46	1425	0.999	0.025	97.5

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1	refinement
XDS		data reduction
XSCALE		data scaling
MoRDa		phasing
PDB_EXTRACT	3.27	data extraction
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1qj5

1qj5

Resolution: 1.9→45.42 Å / SU ML: 0.2561 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.994
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2596	1954	1.58 %	0
R_work	0.2248	121967	-	-
obs	0.2253	123921	99.8 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 45.88 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→45.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11855	0	4	941	12800

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0067	12191
X-RAY DIFFRACTION	f_angle_d	0.7909	16583
X-RAY DIFFRACTION	f_chiral_restr	0.0528	1878
X-RAY DIFFRACTION	f_plane_restr	0.0077	2142
X-RAY DIFFRACTION	f_dihedral_angle_d	13.8267	4395

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 (%)
1.9-1.95	0.3406	133	0.2808	8628	X-RAY DIFFRACTION	98.73
1.95-2	0.3259	134	0.2713	8665	X-RAY DIFFRACTION	99.95
2-2.06	0.2909	127	0.2702	8695	X-RAY DIFFRACTION	99.97
2.06-2.13	0.3178	152	0.2554	8677	X-RAY DIFFRACTION	99.95
2.13-2.2	0.2759	122	0.2503	8701	X-RAY DIFFRACTION	99.89
2.2-2.29	0.26	142	0.2481	8650	X-RAY DIFFRACTION	99.97
2.29-2.39	0.3045	138	0.2474	8749	X-RAY DIFFRACTION	99.91
2.39-2.52	0.2743	137	0.256	8693	X-RAY DIFFRACTION	99.92
2.52-2.68	0.2974	180	0.2554	8656	X-RAY DIFFRACTION	99.91
2.68-2.88	0.273	135	0.2366	8744	X-RAY DIFFRACTION	99.88
2.88-3.17	0.2481	133	0.2278	8704	X-RAY DIFFRACTION	99.88
3.17-3.63	0.2315	143	0.2104	8748	X-RAY DIFFRACTION	99.88
3.63-4.58	0.2154	155	0.182	8767	X-RAY DIFFRACTION	99.84
4.58-45.42	0.2644	123	0.2106	8890	X-RAY DIFFRACTION	99.61

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	1.48300268737	-0.390890529705	-0.160668967753	1.10350912696	-0.311132932543	0.592254193734	0.0285086516607	0.0726320221113	0.144873490091	-0.0623890898332	-0.0335658783287	-0.168529953397	-0.0514038281481	0.0542700756863	0.00831892607847	0.311517328129	-0.0113257512426	0.0237839354119	0.259352813032	-0.0178422021992	0.267418434944	29.7451512368	14.4402624066	-5.883927348
2	2.71433142486	-0.027686394987	0.243779971818	0.738411385518	0.0767604165052	1.4295660167	0.196122764288	-0.605006445642	-0.218449520871	0.174226971303	0.00459045208667	-0.00954176880191	0.133148315225	-0.0206281813238	-0.179184493403	0.39605272724	-0.0535423329043	-0.0112348569384	0.376510748377	0.042368831046	0.376252198965	31.5306849275	-4.03914968616	16.1360800032
3	2.41244623682	-0.0471843984308	0.315755396558	1.04916336228	-0.333445881643	1.46095301545	0.105814515799	0.000122448857397	0.117670333333	-0.0295322888101	-0.065719292782	-0.212455348178	0.0629673258041	0.299609770134	-0.0251595663412	0.280569555458	0.00462434729241	0.0527595460431	0.265588874283	-0.0458267124305	0.304622890575	42.1504485155	7.30405736799	0.845788905069
4	1.54469536204	-0.20217357311	0.195057179265	1.45932657693	0.42853512392	0.779519862534	0.0330883034194	0.0711057418209	-0.141960250764	-0.0917166129455	-0.0501951616498	0.198239788657	-0.00624151875998	-0.0298168506581	0.0106666376227	0.294349252714	-0.00103579672704	-0.00503205194967	0.24131502433	0.00881228213413	0.249587360635	12.9343487059	8.98266297342	-6.08206285605
5	1.71722097304	-0.153420531668	-0.291295172076	1.11964143093	0.40830960527	1.01496330658	0.105420739227	-0.341475350146	0.137617217303	0.178094335262	0.0083516794126	0.0719159399427	-0.100783126008	-0.0315631537878	-0.11557741036	0.419090511283	-0.0348259716653	0.0527658495857	0.310417146283	-0.00321484714028	0.364686058624	11.1210776103	26.9225062427	15.5633313206
6	2.67751410202	0.177326727459	-0.215645047387	0.996723218279	0.376453880266	1.39631067445	0.145238958942	-0.00117578100381	-0.181712163184	-0.0256675133263	-0.105252512504	0.252185873701	-0.103786857575	-0.27492296432	-0.0338951682805	0.306747053824	0.0130398968793	-0.0237719065885	0.261464924928	0.037513537512	0.346949590535	-0.487060439443	15.7937186828	0.792201107803
7	1.82878897499	0.524367370691	-0.443563402519	1.05258843674	0.854340723316	1.32464359926	0.0711011686703	-0.127994268081	0.134422340313	-0.0365091699529	0.0573498779714	-0.0117733844163	-0.274598269165	0.16425578026	-0.137871196835	0.401170077999	-0.0178739766494	-0.00306712671416	0.284594339134	0.0211766717092	0.288151967418	-17.8569321152	26.3508777758	50.8919232278
8	3.03189560133	-0.131235601837	-0.259795064574	1.5997797215	0.167231670487	1.85336342202	0.151943085713	0.129210321087	-0.928309835807	-0.109084663366	-0.0618374467745	-0.0920006513372	0.275398133973	0.249049604077	-0.0799412098004	0.451229500754	0.04798721523	-0.109652424755	0.417660426174	-0.0689093306696	0.550259257891	-16.0132373529	-0.991867710358	36.6682694848
9	2.53675690511	-0.3224926152	0.0546154096725	1.19040826035	0.351546042173	1.4142350566	0.0950507826374	0.034785057673	-0.0484508821247	-0.155544554516	0.0144161047113	-0.117554572454	-0.129608818477	0.275206742708	-0.107499602671	0.366909833331	-0.0440249637867	0.00319277307256	0.367276729928	0.00463356594279	0.293441130186	-7.86017948975	16.7891155492	42.6048566175
10	2.09200925643	-0.60192312531	-0.514709972069	1.07764204107	0.228456822594	1.32928051784	0.0902740326544	0.386118898402	0.148387373253	-0.273151374441	-0.132394155375	0.133368645443	-0.347541366553	-0.281580913171	0.0372184435846	0.449232828193	0.0721977550845	-0.0483652415258	0.354199147255	-0.0214138914112	0.330463755751	-34.2769807179	25.7395817953	46.1289561615
11	0.793605416917	0.176120912692	0.395263622741	1.76938003397	-0.956543469535	1.44323496384	0.0584386234115	-0.315053671184	-0.364958440119	-0.17370125091	0.166637786221	0.168372430887	0.423256530123	-0.302923238811	-0.204191342926	0.516991123362	-0.0451366805026	-0.04212072242	0.475869827926	0.0567742639	0.467540986127	-32.9096210352	4.02963173474	66.951303122
12	1.77910911038	-0.58350756762	0.457522148388	1.67841661773	-0.203507688622	1.77409936657	0.0968628478319	-0.391263027543	-0.320543481688	0.0443157504081	-0.0276345424417	0.372192674098	0.296594985245	-0.377944828875	-0.0595028905808	0.380449979582	-0.0247892396571	-0.00291931857079	0.480571804266	0.0350302586115	0.357981049874	-37.9332094678	11.1627484195	67.0449328264
13	2.17298230376	0.307667039719	0.170357216263	0.66530789467	-0.147829552939	1.55784898813	0.110663592241	0.052621457485	-0.0476196337636	0.00542179389557	-0.0757873995193	0.204804016306	-0.149259912023	-0.429510268051	-0.0447515825417	0.357832908271	0.0899845311372	-0.0329542700593	0.418763417277	-0.0560409239194	0.411245055789	-47.4131352941	19.9677568681	54.3326496769

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 98 )	A	A	1 - 98	1 - 98
2	2	chain 'A' and (resid 99 through 277 )	A	A	99 - 277	99 - 247
3	3	chain 'A' and (resid 278 through 429 )	A	A	278 - 429	248 - 390
4	4	chain 'B' and (resid 1 through 98 )	B	B	1 - 98	1 - 98
5	5	chain 'B' and (resid 99 through 283 )	B	B	99 - 283	99 - 254
6	6	chain 'B' and (resid 284 through 429 )	B	B	284 - 429	255 - 389
7	7	chain 'C' and (resid 1 through 98 )	C	C	1 - 98	1 - 98
8	8	chain 'C' and (resid 99 through 238 )	C	C	99 - 238	99 - 208
9	9	chain 'C' and (resid 239 through 428 )	C	C	239 - 428	209 - 390
10	10	chain 'D' and (resid 1 through 98 )	D	D	1 - 98	1 - 98
11	11	chain 'D' and (resid 99 through 201 )	D	D	99 - 201	99 - 170
12	12	chain 'D' and (resid 202 through 283 )	D	D	202 - 283	171 - 252
13	13	chain 'D' and (resid 284 through 428 )	D	D	284 - 428	253 - 387

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