PDB-7skb: Crystal Structure of aspartate-semialdehyde dehydrogenase from Ac...

ID or keywords:

Entry

Database: PDB / ID: 7skb

Title

Crystal Structure of aspartate-semialdehyde dehydrogenase from Acinetobacter baumannii

Components

Aspartate-semialdehyde dehydrogenase

Keywords

OXIDOREDUCTASE / SSGCID / aspartate-semialdehyde dehydrogenase / Acinetobacter baumannii / reductive dephosphorylation / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / 'de novo' L-methionine biosynthetic process / threonine biosynthetic process / diaminopimelate biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.8 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

United States, 1items

Citation

Journal: to be published
Title: Crystal Structure of aspartate-semialdehyde dehydrogenase from Acinetobacter baumannii
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Oct 20, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 3, 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	7skb.cif.gz	728 KB	Display	PDBx/mmCIF format
PDB format	pdb7skb.ent.gz	497.4 KB	Display	PDB format
PDBx/mmJSON format	7skb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7skb_validation.pdf.gz	458.8 KB	Display	wwPDB validaton report
Full document	7skb_full_validation.pdf.gz	464 KB	Display
Data in XML	7skb_validation.xml.gz	66.8 KB	Display
Data in CIF	7skb_validation.cif.gz	100.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sk/7skb ftp://data.pdbj.org/pub/pdb/validation_reports/sk/7skb	HTTPS FTP

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Related structure data

Related structure data	3uw3S S: Starting model for refinement
Similar structure data	6i5z-1 4r5m-d 5jr3-2 6clw-d 1oy7-d 1x1c-2 6t8y-2 4m71-d 4qfd-1 3i58-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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: Aspartate-semialdehyde dehydrogenase

B: Aspartate-semialdehyde dehydrogenase

C: Aspartate-semialdehyde dehydrogenase

D: Aspartate-semialdehyde dehydrogenase

hetero molecules

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

1

A: Aspartate-semialdehyde dehydrogenase

B: Aspartate-semialdehyde dehydrogenase

hetero molecules

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

2

C: Aspartate-semialdehyde dehydrogenase

D: Aspartate-semialdehyde dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	48.120, 84.620, 189.480
Angle α, β, γ (deg.)	90.000, 93.936, 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

#1: Protein	Aspartate-semialdehyde dehydrogenase / ASA dehydrogenase / ASADH / Aspartate-beta-semialdehyde dehydrogenase Mass: 41637.734 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: ABUW_3451 / Plasmid: AcbaC.17885.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: V5VGT0, aspartate-semialdehyde dehydrogenase
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1540 / 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: 2.32 Å³/Da / Density % sol: 46.95 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Molecular Dimensions / Calibre MCSG1 screen, conditions G4: 200mM potassium / sodium tartrate, 20% (w/V) PEG 3350: AcbaC.17885.a.B1.PW38925 at 18mg/ml + 3mM NAD. Tray 320156 g4, cryo: 20% EG ...Details: Molecular Dimensions / Calibre MCSG1 screen, conditions G4: 200mM potassium / sodium tartrate, 20% (w/V) PEG 3350: AcbaC.17885.a.B1.PW38925 at 18mg/ml + 3mM NAD. Tray 320156 g4, cryo: 20% EG + 3mM NAD: puck noh5-9

Crystal

Density Matthews: 2.32 Å³/Da / Density % sol: 46.95 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Molecular Dimensions / Calibre MCSG1 screen, conditions G4: 200mM potassium / sodium tartrate, 20% (w/V) PEG 3350: AcbaC.17885.a.B1.PW38925 at 18mg/ml + 3mM NAD. Tray 320156 g4, cryo: 20% EG ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-G / Wavelength: 0.97856 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 29, 2021 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97856 Å / Relative weight: 1

Reflection

Resolution: 1.8→50 Å / Num. obs: 140224 / % possible obs: 99.9 % / Redundancy: 4.158 % / B_iso Wilson estimate: 30.462 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.051 / R_rim(I) all: 0.059 / Χ²: 0.946 / Net I/σ(I): 16.88

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
1.8-1.85	4.182	0.522	2.49	10323	0.801	0.6	100
1.85-1.9	4.19	0.405	3.3	10006	0.88	0.465	99.9
1.9-1.95	4.189	0.306	4.37	9819	0.92	0.351	99.9
1.95-2.01	4.201	0.24	5.58	9565	0.952	0.275	100
2.01-2.08	4.203	0.194	7.04	9209	0.968	0.223	99.9
2.08-2.15	4.197	0.151	8.86	8898	0.981	0.173	100
2.15-2.23	4.205	0.12	11.16	8624	0.986	0.137	99.9
2.23-2.32	4.185	0.101	13.07	8315	0.991	0.116	99.9
2.32-2.43	4.194	0.085	15.14	8002	0.993	0.098	99.9
2.43-2.55	4.184	0.075	17.38	7590	0.994	0.087	99.9
2.55-2.68	4.174	0.062	20.17	7248	0.996	0.072	99.9
2.68-2.85	4.17	0.054	23.05	6868	0.997	0.062	99.8
2.85-3.04	4.133	0.045	27.14	6467	0.998	0.052	99.9
3.04-3.29	4.085	0.038	31.96	5970	0.998	0.043	99.9
3.29-3.6	4.065	0.031	36.69	5541	0.999	0.036	99.9
3.6-4.02	4.042	0.027	39.24	5045	0.999	0.031	99.9
4.02-4.65	4.09	0.025	42.46	4413	0.999	0.028	99.9
4.65-5.69	4.063	0.025	42.14	3775	0.999	0.028	100
5.69-8.05	4.032	0.024	41.39	2946	0.999	0.028	100
8.05-50	3.749	0.021	43.25	1600	0.999	0.024	97

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.20rc1	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3uw3 as per Morda

3uw3

Resolution: 1.8→31.07 Å / SU ML: 0.1676 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7766
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1737	2058	1.47 %	0
R_work	0.143	138110	-	-
obs	0.1434	140168	99.88 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 27.62 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→31.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11289	0	40	1542	12871

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0084	11842
X-RAY DIFFRACTION	f_angle_d	0.927	16155
X-RAY DIFFRACTION	f_chiral_restr	0.0632	1876
X-RAY DIFFRACTION	f_plane_restr	0.008	2087
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1922	4414

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 (%)
1.8-1.84	0.2811	137	0.213	9158	X-RAY DIFFRACTION	99.91
1.84-1.89	0.2259	116	0.1852	9119	X-RAY DIFFRACTION	99.91
1.89-1.94	0.2344	132	0.1729	9195	X-RAY DIFFRACTION	99.91
1.94-2	0.2215	125	0.1589	9203	X-RAY DIFFRACTION	99.93
2-2.06	0.1764	141	0.152	9154	X-RAY DIFFRACTION	99.92
2.06-2.13	0.1717	121	0.1459	9191	X-RAY DIFFRACTION	99.94
2.13-2.22	0.1848	136	0.1422	9175	X-RAY DIFFRACTION	99.95
2.22-2.32	0.1875	172	0.1467	9198	X-RAY DIFFRACTION	99.88
2.32-2.44	0.1885	116	0.1443	9200	X-RAY DIFFRACTION	99.9
2.44-2.6	0.1863	142	0.1509	9195	X-RAY DIFFRACTION	99.93
2.6-2.8	0.1737	103	0.1542	9278	X-RAY DIFFRACTION	99.86
2.8-3.08	0.177	163	0.1533	9154	X-RAY DIFFRACTION	99.9
3.08-3.52	0.1693	187	0.1366	9216	X-RAY DIFFRACTION	99.91
3.52-4.44	0.151	155	0.1177	9280	X-RAY DIFFRACTION	99.9
4.44-31.07	0.1406	112	0.1333	9394	X-RAY DIFFRACTION	99.51

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	2.79912179859	-0.311930004186	0.0545417040727	0.743445780929	-0.255317534749	2.22066034396	0.00336048669442	0.116315070248	-0.169148331815	-0.0939959335635	-0.0473751090012	-0.0947060172335	0.238066726687	0.234926386319	0.0398567719033	0.202966462579	0.0273546278428	0.030069067828	0.136977180236	-0.00478125455576	0.208036178308	6.16589718109	-12.2263307991	70.9401134029
2	0.467445319272	0.051275709357	0.0212939627414	0.720395864869	0.192039621505	0.761157018069	-0.0128836191578	0.0650783684463	-0.0383125169687	-0.0489029845711	-0.0157034898469	-0.0152238520687	0.0186066642491	-0.0249257300791	0.0250339585321	0.124830890262	0.00641174261081	0.014876766725	0.155586216153	0.00314522657533	0.151165042718	-10.161945281	9.27687555836	70.0343470636
3	1.90728873461	-0.297092991205	-0.31128367972	0.932579796872	0.507278775061	1.87664322978	0.0399237699977	0.109069805104	0.150085202726	-0.286676699054	-0.133549490783	0.243050537576	-0.276058033133	-0.315351895871	0.0767596693289	0.276972412425	0.082560821518	-0.0713309925576	0.18672434576	-0.00493721428272	0.305282029184	-27.1530284791	46.8956062745	77.4706378531
4	0.510439843129	0.092061558244	0.0646680302722	0.620633428212	0.00280160248919	1.16669459806	-0.019890107718	0.0389407045783	0.0632267872855	-0.0435983659948	-0.0197782435124	0.0722190323344	-0.108504845376	-0.132960434574	0.0216158614353	0.156081460736	0.0171532482685	0.00593368740827	0.174040829331	-0.00636532711592	0.182111213029	-16.0229134799	20.3835984707	74.2514759964
5	0.937088402937	-0.293305148475	-0.220675051101	1.26703809119	0.312841722487	1.03843379141	0.00371033168345	0.10850206393	0.197482446978	-0.237582450438	0.00822320466915	-0.0933729801361	-0.290145633327	0.0255887524761	-0.00987187564269	0.229408080447	-0.00327048417906	0.00223407788722	0.156979924535	0.0507724591958	0.181841058106	-7.49148411848	33.6127848676	63.9431976759
6	3.20834123687	0.520169333025	0.376325081324	1.73762898919	-0.409092740829	2.56972373057	0.00129966977419	0.105477300127	0.321627920644	0.0340525675003	-0.0980805670636	-0.135278615061	-0.387854223928	0.292255622306	0.0923190587951	0.225325317218	-0.0402153652126	-0.0197009443761	0.178064397667	0.0290094848603	0.200697349787	13.0780288287	12.9674358574	16.7884433291
7	4.46170292337	0.249784983995	-0.769899607968	0.72456005269	-0.462888113678	1.6963467931	0.0883552036848	-0.623051585252	-0.0801540034915	0.167558547003	-0.110307423935	-0.0914112487706	-0.161487316729	0.342949993242	0.00977605007956	0.21377514676	-0.0388350027438	-0.043012969695	0.239152784557	-0.0273310874483	0.199448838208	11.6777391647	7.38040162023	32.769943787
8	0.535217601319	-0.104496778231	-0.194769362943	0.637543828687	0.342331905396	1.3449603355	-0.00504631718196	-0.0506073404464	-0.00512130546239	0.00559832778869	0.0216218089482	-0.0800883039507	0.0502661787509	0.112393615094	-0.0341397119028	0.15385036945	0.00478750821863	-0.00979247407701	0.171108221359	0.0111504886535	0.175548392426	1.58383746455	-17.0935010149	19.7674168939
9	0.860501566593	0.152612308815	-0.190448008123	1.10204980821	-0.0651826246925	0.938560362093	0.0100896971266	-0.101700871595	0.120299515689	0.1018714916	-0.0182922653745	0.0872565226637	-0.0728379788933	-0.105932135679	0.010783687301	0.152695818998	0.00844833872161	-0.0105834833565	0.190558030918	-0.0267533508789	0.169045467503	-8.97146039617	-4.61331498361	29.2083094889
10	1.59157594758	0.337195005158	0.274722574921	0.829356982497	0.417219508469	1.86697946186	0.0398021446917	-0.0885142210464	-0.0877840265748	0.311104549996	-0.152327659372	0.28126317342	0.374352322845	-0.379831118452	0.093521162951	0.297100628409	-0.0893131782006	0.0788953055602	0.204347360713	-0.0261123014132	0.280859845017	-20.7799811896	-48.4027923209	16.9862430716
11	0.51981232361	0.00144349412995	-0.01158088075	0.798572024723	0.000509791921406	0.995966959372	-0.0243907841605	-0.0566135583664	-0.0634065757866	0.0885041349405	-0.0182395729723	0.0482777835457	0.161391263782	-0.0545247144899	0.034645524838	0.153243007314	-0.00754755610434	0.00438421224904	0.150491866891	-0.00194193119041	0.141961053532	-6.29422186327	-26.8788276357	23.9875977666

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 134 )	A	A	-1 - 134	1 - 136
2	2	chain 'A' and (resid 135 through 371 )	A	A	135 - 371	137 - 373
3	3	chain 'B' and (resid -1 through 134 )	B	C	-1 - 134	1 - 136
4	4	chain 'B' and (resid 135 through 282 )	B	C	135 - 282	137 - 284
5	5	chain 'B' and (resid 283 through 372 )	B	C	283 - 372	285 - 374
6	6	chain 'C' and (resid 0 through 74 )	C	E	0 - 74	1 - 75
7	7	chain 'C' and (resid 75 through 134 )	C	E	75 - 134	76 - 135
8	8	chain 'C' and (resid 135 through 252 )	C	E	135 - 252	136 - 253
9	9	chain 'C' and (resid 253 through 371 )	C	E	253 - 371	254 - 372
10	10	chain 'D' and (resid -1 through 134 )	D	G	-1 - 134	1 - 136
11	11	chain 'D' and (resid 135 through 371 )	D	G	135 - 371	137 - 373

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