PDB-7s5m: Crystal Structure of a 8-amino-7-oxononanoate synthase/2-amino-3-...

ID or keywords:

Entry

Database: PDB / ID: 7s5m

Title

Crystal Structure of a 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase from Mycobacterium smegmatis

Components

8-amino-7-oxononanoate synthase

Keywords

TRANSFERASE / SSGCID / 8-amino-7-oxononanoate synthase / 2-amino-3-ketobutyrate coenzyme A ligase / Mycolicibacterium smegmatis / Mycobacterium smegmatis / bioF / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

8-amino-7-oxononanoate synthase / 8-amino-7-oxononanoate synthase activity / biotin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.25 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of a 8-amino-7-oxononanoate synthase/2-amino-3-ketobutyrate coenzyme A ligase from Mycobacterium smegmatis
Authors: Abendroth, J. / Davies, D.R. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Sep 10, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 22, 2021	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	7s5m.cif.gz	638.2 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	7s5m_validation.pdf.gz	455.8 KB	Display	wwPDB validaton report
Full document	7s5m_full_validation.pdf.gz	465 KB	Display
Data in XML	7s5m_validation.xml.gz	50.4 KB	Display
Data in CIF	7s5m_validation.cif.gz	71.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/s5/7s5m ftp://data.pdbj.org/pub/pdb/validation_reports/s5/7s5m	HTTPS FTP

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Related structure data

Related structure data	3wy7S S: Starting model for refinement
Similar structure data	7s5m-2 1fc4-d 7bxr-d 6hx7-2 5dex-d 2zgz-d 5jay-d 6oia-2 6ed7-3 7bxs-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

Deposited unit

A: 8-amino-7-oxononanoate synthase

B: 8-amino-7-oxononanoate synthase

C: 8-amino-7-oxononanoate synthase

D: 8-amino-7-oxononanoate synthase

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

1

A: 8-amino-7-oxononanoate synthase

B: 8-amino-7-oxononanoate synthase

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

2

C: 8-amino-7-oxononanoate synthase

D: 8-amino-7-oxononanoate synthase

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

Unit cell

Length a, b, c (Å)	60.710, 108.940, 108.340
Angle α, β, γ (deg.)	90.000, 94.651, 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

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 7 through 15 or (resid 16...
d_2	ens_1	(chain "B" and (resid 7 through 9 or (resid 10...
d_3	ens_1	(chain "C" and (resid 7 through 9 or (resid 10...
d_4	ens_1	(chain "D" and (resid 7 through 9 or (resid 10...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	LEU	LEU	A	1 - 23
d_1	2	ens_1	VAL	LEU	A	25 - 43
d_1	3	ens_1	GLN	ALA	A	45 - 284
d_1	4	ens_1	ALA	ILE	A	286 - 312
d_1	5	ens_1	PRO	THR	A	316 - 374
d_2	1	ens_1	LEU	LEU	B	3 - 25
d_2	2	ens_1	VAL	LEU	B	27 - 45
d_2	3	ens_1	GLN	ALA	B	47 - 286
d_2	4	ens_1	ALA	ILE	B	288 - 314
d_2	5	ens_1	PRO	THR	B	318 - 376
d_3	1	ens_1	LEU	LEU	C	3 - 25
d_3	2	ens_1	VAL	LEU	C	27 - 45
d_3	3	ens_1	GLN	ALA	C	47 - 286
d_3	4	ens_1	ALA	ILE	C	288 - 314
d_3	5	ens_1	PRO	THR	C	318 - 376
d_4	1	ens_1	LEU	LEU	D	1 - 23
d_4	2	ens_1	VAL	LEU	D	25 - 43
d_4	3	ens_1	GLN	ALA	D	45 - 284
d_4	4	ens_1	ALA	THR	D	286 - 371

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.254591700586, -0.967004559795, 0.00923294803184), (-0.966989668964, 0.254459138199, -0.0134731995008), (0.0106792373531, -0.0123583301341, -0.999866603886)	26.6953017877, 21.3451002805, 60.4556585594
2	given	(0.999999813603, -0.000407850561738, -0.000454369759444), (-0.000396538947839, -0.999696726564, 0.0246231122103), (-0.000464274511312, -0.0246229274453, -0.999696701952)	30.3703363092, -47.1916187558, 55.5100524329
3	given	(-0.256772558738, -0.966396874041, 0.0120388921361), (0.966366245063, -0.256908726902, -0.0115838873113), (0.0142875289388, 0.00865955460323, 0.999860429575)	56.9905670565, -67.0035967414, -5.51587772635

#1: Protein	8-amino-7-oxononanoate synthase / AONS / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7- ...AONS / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7-ketopelargonate synthase / Alpha-oxoamine synthase Mass: 41777.316 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria) Strain: ATCC 700084 / mc(2)155 / Gene: bioF, MSMEG_3189, MSMEI_3107 / Plasmid: MysmA.00272.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0QX65, 8-amino-7-oxononanoate synthase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

8-amino-7-oxononanoate synthase / AONS / 7-keto-8-amino-pelargonic acid synthase / 7-KAP synthase / KAPA synthase / 8-amino-7- ...

Mass: 41777.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) (bacteria)
Strain: ATCC 700084 / mc(2)155 / Gene: bioF, MSMEG_3189, MSMEI_3107 / Plasmid: MysmA.00272.a.A1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0QX65, 8-amino-7-oxononanoate synthase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.14 Å³/Da / Density % sol: 42.6 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: Hampton Research PACT screen, condition F7: 200mM Sodium acetate, 100mM BisTris propane pH 6.5, 20% (w/V) PEG 3350: MysmA.00272.a.A1.PW28493 at 24.73mg/ml: tray 215578 F7: cryo: 20% EG: puck KFC7-1

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.2 / Wavelength: 0.9795 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 30, 2010 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9795 Å / Relative weight: 1

Reflection

Resolution: 2.25→50 Å / Num. obs: 65861 / % possible obs: 98.8 % / Redundancy: 4.536 % / B_iso Wilson estimate: 44.62 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.087 / R_rim(I) all: 0.098 / Χ²: 0.901 / Net I/σ(I): 11.07

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
2.25-2.31	4.603	0.621	2.31	4777	0.837	0.702	97.5
2.31-2.37	4.633	0.492	2.79	4680	0.887	0.555	98.5
2.37-2.44	4.628	0.438	3.15	4642	0.894	0.494	98.8
2.44-2.52	4.592	0.384	3.62	4449	0.908	0.434	98.3
2.52-2.6	4.645	0.322	4.33	4316	0.945	0.363	98.8
2.6-2.69	4.597	0.267	5.12	4175	0.957	0.302	98.8
2.69-2.79	4.596	0.221	6.23	4111	0.972	0.249	99
2.79-2.9	4.571	0.186	7.43	3862	0.975	0.211	98.8
2.9-3.03	4.553	0.151	9.09	3764	0.984	0.17	99.2
3.03-3.18	4.521	0.115	11.41	3582	0.99	0.129	99.1
3.18-3.35	4.492	0.089	14.32	3386	0.994	0.1	98.5
3.35-3.56	4.461	0.073	17.18	3233	0.995	0.082	99.2
3.56-3.8	4.437	0.06	19.74	3034	0.996	0.068	98.9
3.8-4.11	4.443	0.052	22.44	2831	0.996	0.059	99
4.11-4.5	4.45	0.046	24.66	2607	0.997	0.052	99.4
4.5-5.03	4.396	0.045	25.5	2381	0.997	0.05	99.4
5.03-5.81	4.312	0.05	23.17	2095	0.997	0.057	99.4
5.81-7.12	4.389	0.047	24.04	1776	0.998	0.053	99.4
7.12-10.06	4.482	0.039	28.35	1406	0.998	0.043	99.7
10.06-50	4.199	0.041	28.22	754	0.998	0.046	96.3

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.18 4274	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3wy7 as per Morda

3wy7

Resolution: 2.25→46.23 Å / SU ML: 0.3355 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.8029
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2743	1885	2.87 %	0
R_work	0.2302	63909	-	-
obs	0.2315	65794	98.74 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 47.33 Å²

Refinement step

Cycle: LAST / Resolution: 2.25→46.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10504	0	0	213	10717

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	10664
X-RAY DIFFRACTION	f_angle_d	0.9238	14571
X-RAY DIFFRACTION	f_chiral_restr	0.0533	1802
X-RAY DIFFRACTION	f_plane_restr	0.0089	1936
X-RAY DIFFRACTION	f_dihedral_angle_d	11.554	3664

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.433290533005
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.304845014895
ens_1	d_4	A	X-RAY DIFFRACTION	Torsion NCS	0.421686821654

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 (%)
2.25-2.31	0.3958	143	0.3096	4792	X-RAY DIFFRACTION	97.24
2.31-2.38	0.3618	152	0.2787	4873	X-RAY DIFFRACTION	98.55
2.38-2.46	0.2713	137	0.2704	4907	X-RAY DIFFRACTION	98.77
2.46-2.54	0.3328	126	0.2682	4900	X-RAY DIFFRACTION	98.28
2.54-2.65	0.3032	141	0.2707	4926	X-RAY DIFFRACTION	98.73
2.65-2.77	0.3512	141	0.2606	4903	X-RAY DIFFRACTION	98.75
2.77-2.91	0.3229	147	0.258	4902	X-RAY DIFFRACTION	98.84
2.91-3.09	0.329	119	0.2536	4923	X-RAY DIFFRACTION	98.98
3.09-3.33	0.2955	162	0.2461	4904	X-RAY DIFFRACTION	98.69
3.33-3.67	0.2515	179	0.2239	4925	X-RAY DIFFRACTION	99.13
3.67-4.2	0.2673	182	0.2057	4876	X-RAY DIFFRACTION	98.96
4.2-5.29	0.2201	140	0.1935	4995	X-RAY DIFFRACTION	99.36
5.29-46.23	0.2224	116	0.2096	5083	X-RAY DIFFRACTION	99.29

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	2.14829341436	0.266384531977	-0.421152053536	1.88742781104	0.0457035064874	0.967702177681	-0.0437433194586	-0.121042555448	-0.174565481334	0.0545855648104	0.0364042643637	-0.0486800407797	0.216328747891	0.132212439556	-0.00427767264571	0.321136654861	0.0411339117989	-0.0229765553916	0.239726055148	0.00368665574375	0.234655563409	17.1284289073	-4.67125000268	40.2258269462
2	2.59962237022	0.775385589957	0.136140094692	1.76389219533	-0.263007832138	0.647849824365	0.0175106910917	-0.0648626568304	-0.112676796359	-0.0985551787331	0.0521908316686	0.228899842694	0.116425693048	-0.109511794782	-0.0773241296388	0.288065796323	0.0355341464387	-0.0425485943264	0.230852979979	0.0239990267214	0.241261563911	3.43239814088	-7.15360185535	37.0845444452
3	1.95490132652	-0.446017847104	-0.211851519156	1.54717429819	0.123510838609	0.952181474686	0.0196787733675	0.252521527639	0.0711598219391	-0.007575035441	-0.0403640896921	-0.0830422122907	0.137940193028	0.00842732118893	0.0285035134188	0.264342147081	0.0247012983102	-0.00119351003932	0.254032962597	0.0196180690753	0.271506747706	26.2573466754	4.18385120922	20.5105466282
4	3.46065630858	0.230969602375	-0.472776677197	2.69799895491	1.12362215187	3.04088196448	-0.111272708377	-0.244158715753	0.310637882037	0.511770939067	0.300215822583	-0.689469748651	0.0287901500956	0.508617681683	-0.149050406411	0.304621636778	0.00975477040459	-0.0771214386433	0.404681206869	-0.0582259239209	0.788288657358	42.0443240841	21.1088249778	27.8670593382
5	1.93155561837	0.68795954624	0.149433139913	1.83625509988	-0.201544916723	0.742510317006	-0.100837220557	0.201066828922	0.00879850439562	0.0242219938376	0.139375207551	-0.104976897641	-0.219560221772	0.110647824729	-0.0262761954936	0.401145137989	-0.0257033830105	-0.00790465855204	0.278827196176	0.00601506583736	0.264323641205	47.6139563361	-43.3478825666	20.2237941564
6	1.8622745549	0.0669836236851	-0.330921276239	1.12571366099	0.568832806548	0.411318727092	-0.118802865523	0.485868148598	0.106878835593	-0.1864056358	0.0826987393277	-0.0386089421144	-0.145870665307	0.0952034129995	0.0274913233044	0.402753307348	-0.114781058133	-0.00443586261744	0.413446799163	0.0393401406014	0.225183882249	45.6619947392	-42.3574306404	9.57825403755
7	2.81901390707	0.197506093271	0.228536407352	3.01698708165	0.629158872904	1.98985671283	-0.0444057285861	-0.118067639214	0.194942866951	0.418036750092	0.0827862167726	0.214102043153	0.0404126354102	-0.0417617626584	-0.02744088898	0.391398396604	0.0466845523541	0.0740712447638	0.29668199282	0.0534407538261	0.489895851547	26.5353579141	-31.4762702795	23.1581417887
8	1.40355100474	1.01014833479	-0.399988385011	3.4754742276	-0.697490231551	1.00137511986	-0.105429494291	0.413407693273	-0.195064457385	-0.227731421721	0.330107477057	-0.49678150516	-0.0890468322064	0.246191899694	0.0898548325052	0.547326116818	-0.109694955056	0.0909151493441	0.4346353594	-0.0101231286576	0.551529023844	65.6084095756	-55.3424499311	11.5607851548
9	2.12298516241	0.903335015188	0.14275291905	2.36854160097	0.131708586957	1.66544504182	-0.0704039216731	-0.0059217440842	0.110298068847	-0.0859511776022	-0.0905489167483	0.217473886195	-0.176433540619	-0.272110799559	-0.00163124979592	0.271170825632	-0.0145979844093	-0.0218689695738	0.282025730825	0.0238647391278	0.32652576869	42.7037188667	-57.5026721413	33.5272443221
10	1.31460174369	0.716526877785	0.026078447901	2.10208936952	-0.605235188783	0.979572817179	-0.0635994572662	-0.0874557827668	0.318580577526	0.181494718793	0.0586003529	-0.245790110707	-0.271925021146	0.238949710424	0.0164228886742	0.346808973921	-0.00361213341956	-0.069154066894	0.304113059142	-0.0196690041985	0.35541743117	60.8845799675	-41.2633854426	35.0887603613
11	1.65449274693	0.902135409771	0.314816997203	2.71081848435	-0.316914640416	1.72773513917	0.132814310232	-0.244118279971	-0.0806249983343	0.607601105643	-0.125615553391	-0.461417790395	-0.195895907524	0.156643678889	0.0106615782387	0.425107994626	-0.0318334277843	-0.081051850373	0.349681435254	0.0238080342892	0.383037303164	62.2258565921	-47.6644964066	43.6170220564
12	1.44385969257	0.821304302078	-0.0578950174956	2.96956023885	-0.552948775745	0.123467278246	-0.073482876461	0.0412299209849	0.300204192936	-0.219253420277	0.00386948480612	0.520197037183	-0.473606290139	-0.0434429781881	0.00739039981895	0.490682429666	-0.00848287679526	0.0211579364026	0.309726898087	0.0772802556429	0.364194997518	46.5168179157	-41.3747453306	35.2781857618
13	2.30316917594	0.0203058080058	0.602137442085	2.33212193151	0.543792333768	0.952851387383	0.0716511829388	-0.231573490532	-0.593833167829	-0.0280322744726	0.130299842566	-0.669816674013	0.054588587054	0.184015312232	-0.207346675503	0.338893754818	-0.0319218290384	-0.00667142923254	0.267149427407	0.0515899991449	0.612705905518	63.1182536709	-66.763180264	34.1468790453
14	2.81456410983	0.421248540166	0.0830239737568	3.4913930283	0.71474877803	2.78934352246	0.148101014514	0.303184024448	-0.592559527301	-0.465860746041	0.312889526091	-1.04421244649	-0.659350617575	0.336192475075	-0.282447113458	0.547916347248	-0.00722523930205	0.0834766375011	0.397980389093	-0.0997478196655	1.02238896459	70.5769991066	-68.3500978157	27.2360384106

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 7 through 242 )	A	A	7 - 242	1 - 236
2	2	chain 'A' and (resid 243 through 383 )	A	A	243 - 383	237 - 377
3	3	chain 'B' and (resid 5 through 304 )	B	B	5 - 304	1 - 300
4	4	chain 'B' and (resid 305 through 382 )	B	B	305 - 382	301 - 378
5	5	chain 'C' and (resid 5 through 160 )	C	C	5 - 160	1 - 156
6	6	chain 'C' and (resid 161 through 304 )	C	C	161 - 304	157 - 300
7	7	chain 'C' and (resid 305 through 383 )	C	C	305 - 383	301 - 379
8	8	chain 'D' and (resid 7 through 41 )	D	D	7 - 41	1 - 35
9	9	chain 'D' and (resid 42 through 94 )	D	D	42 - 94	36 - 88
10	10	chain 'D' and (resid 95 through 151 )	D	D	95 - 151	89 - 145
11	11	chain 'D' and (resid 152 through 242 )	D	D	152 - 242	146 - 236
12	12	chain 'D' and (resid 243 through 269 )	D	D	243 - 269	237 - 263
13	13	chain 'D' and (resid 270 through 335 )	D	D	270 - 335	264 - 326
14	14	chain 'D' and (resid 336 through 380 )	D	D	336 - 380	327 - 371

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