PDB-6wop: Crystal structure of gamma-aminobutyrate aminotransferase PuuE fr...

ID or keywords:

Entry

Database: PDB / ID: 6wop

Title

Crystal structure of gamma-aminobutyrate aminotransferase PuuE from Acinetobacter baumannii

Components

4-aminobutyrate transaminase

Keywords

TRANSFERASE / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES

Function / homology

Function and homology information

4-aminobutyrate-2-oxoglutarate transaminase / 4-aminobutyrate:2-oxoglutarate transaminase activity / gamma-aminobutyric acid metabolic process / pyridoxal phosphate binding
Similarity search - Function

Biological species

Acinetobacter baumannii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Stogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: Crystal structure of gamma-aminobutyrate aminotransferase PuuE from Acinetobacter baumannii
Authors: Stogios, P.J.

History

Deposition	Apr 25, 2020	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 13, 2020	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6wop.cif.gz	390.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6wop.ent.gz	279.8 KB	Display	PDB format
PDBx/mmJSON format	6wop.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6wop_validation.pdf.gz	457.7 KB	Display	wwPDB validaton report
Full document	6wop_full_validation.pdf.gz	465.8 KB	Display
Data in XML	6wop_validation.xml.gz	41.9 KB	Display
Data in CIF	6wop_validation.cif.gz	64.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wo/6wop ftp://data.pdbj.org/pub/pdb/validation_reports/wo/6wop	HTTPS FTP

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Related structure data

Related structure data	1sffS S: Starting model for refinement
Similar structure data	7jh3-2 1sf2-d 7jh3-1 1szk-d 6wj8-d 1sff-d 1szu-d 1szs-d 4atp-1 6rl5-2 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
Other databases	TargetTrack: IDP96275

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#198 - Jun 2016 Beta-galactosidase similarity (1)

Deposited unit

A: 4-aminobutyrate transaminase

B: 4-aminobutyrate transaminase

hetero molecules

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

1

A: 4-aminobutyrate transaminase

B: 4-aminobutyrate transaminase

hetero molecules

A: 4-aminobutyrate transaminase

B: 4-aminobutyrate transaminase

hetero molecules

defined by author&software
185 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	92.379, 188.453, 114.113
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁
Space group name Hall	C2c2
Symmetry operation	#1: x,y,z #2: x,-y,-z #3: -x,y,-z+1/2 #4: -x,-y,z+1/2 #5: x+1/2,y+1/2,z #6: x+1/2,-y+1/2,-z #7: -x+1/2,y+1/2,-z+1/2 #8: -x+1/2,-y+1/2,z+1/2

Components on special symmetry positions

ID	Model	Components
1	1	B-738- HOH
2	1	B-1042- HOH

#1: Protein	4-aminobutyrate transaminase / PuuE Mass: 45967.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Acinetobacter baumannii (strain ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81) (bacteria) Strain: ATCC 19606 / DSM 30007 / CIP 70.34 / JCM 6841 / NBRC 109757 / NCIMB 12457 / NCTC 12156 / 81 Gene: gabT, HMPREF0010_02436 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Magic References: UniProt: D0CCF6, 4-aminobutyrate-2-oxoglutarate transaminase
#2: Chemical	ChemComp-TAR / D(-)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₆
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / 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: 2.7 Å³/Da / Density % sol: 54.46 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 20% (w/v) PEG3350, 0.2M potassium sodium tartrate, 5 mM Glutamic acid

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 11, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 1.85→20 Å / Num. obs: 84930 / % possible obs: 100 % / Redundancy: 8 % / B_iso Wilson estimate: 21.45 Å² / R_merge(I) obs: 0.112 / R_pim(I) all: 0.042 / Net I/σ(I): 20.5
Reflection shell	Resolution: 1.85→1.88 Å / R_merge(I) obs: 0.384 / Mean I/σ(I) obs: 2.05 / Num. unique obs: 4194 / CC_1/2: 0.919 / R_pim(I) all: 0.272 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.15_3448	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing
PHENIX		model building
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1SFF

1sff

Resolution: 1.85→19.96 Å / SU ML: 0.1797 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.906
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2223	1998	2.36 %	RANDOM
R_work	0.1809	82789	-	-
obs	0.1819	84787	99.77 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 26.96 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→19.96 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6280	0	41	941	7262

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0176	6483
X-RAY DIFFRACTION	f_angle_d	1.4127	8800
X-RAY DIFFRACTION	f_chiral_restr	0.102	994
X-RAY DIFFRACTION	f_plane_restr	0.0106	1162
X-RAY DIFFRACTION	f_dihedral_angle_d	19.7349	2326

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 (%)
1.85-1.9	0.2712	139	0.2356	5753	X-RAY DIFFRACTION	98.51
1.9-1.95	0.2456	142	0.2151	5885	X-RAY DIFFRACTION	99.9
1.95-2	0.2555	141	0.2063	5866	X-RAY DIFFRACTION	99.97
2-2.07	0.2364	143	0.1944	5885	X-RAY DIFFRACTION	99.8
2.07-2.14	0.2376	140	0.1861	5858	X-RAY DIFFRACTION	99.83
2.14-2.23	0.2255	143	0.1797	5883	X-RAY DIFFRACTION	99.93
2.23-2.33	0.2429	142	0.1825	5898	X-RAY DIFFRACTION	99.98
2.33-2.45	0.2524	141	0.1818	5875	X-RAY DIFFRACTION	99.9
2.45-2.61	0.2158	142	0.1791	5891	X-RAY DIFFRACTION	99.88
2.61-2.81	0.2494	143	0.1841	5939	X-RAY DIFFRACTION	99.95
2.81-3.09	0.2036	144	0.1806	5959	X-RAY DIFFRACTION	99.92
3.09-3.53	0.1835	143	0.174	5931	X-RAY DIFFRACTION	99.88
3.53-4.44	0.2078	145	0.1587	6003	X-RAY DIFFRACTION	99.81
4.44-19.96	0.2198	150	0.1821	6163	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	6.26689503074	1.19881141543	-0.612968495478	0.546459966093	-1.07183262768	2.94350376296	0.201254252895	-0.362809422003	-0.00224608026189	0.503561577757	-0.154130867576	-0.222757813061	-0.272076462234	0.289152103251	-0.0341980995031	0.350695924581	-0.0287406281314	-0.0395758353725	0.264707631733	-0.016446621218	0.131337579073	7.64291462685	30.393840219	22.022984517
2	1.92824558054	0.0586668756732	0.878596462112	1.76364551784	0.234439911477	0.753687589621	0.015674303346	-0.0425220937389	0.0662154297599	-0.0188664202504	-0.0399065729162	-0.128512651294	-0.0486519594096	-0.0456531084987	0.03510763606	0.133384477081	-0.00958950353689	0.0389041174311	0.132035457964	-0.00783311876667	0.0960938481765	8.25345139226	38.1570725505	-2.29106347659
3	0.402270156893	0.0449209195126	0.148463236595	1.74795088728	-0.242083110374	0.350488006895	0.0306038246775	-0.0570171398985	-0.029218331965	0.0631780216776	-0.0260071880484	-0.0815113517538	0.00161157970731	-0.0493295862549	-0.00208131133973	0.135356798344	0.00361173729388	0.0133230450225	0.194664517644	-0.0361350425814	0.127911079094	8.62209302013	12.8938530287	-3.83042648682
4	2.83221906996	1.38542247839	0.172085650344	2.8047448309	-0.0198899838327	0.0551495674433	-0.0155473383128	-0.0347375348454	-0.22375316685	-0.183844381798	0.0235401090569	-0.573244126904	0.0345814654517	0.150223059888	-0.0148211887254	0.145014506067	0.00963096027441	0.0378945440275	0.194547263708	-0.00635181217362	0.227455875845	21.6417926877	7.40789311514	-5.72733522631
5	0.197169622396	-0.0584769209074	0.142599603167	2.25310761647	0.158282361748	0.198054704406	0.0516718066233	0.0907116814265	-0.0291414189074	-0.328201916075	-0.0215437042508	-0.291706524621	-0.0317003411106	0.0108476114121	-0.0270845679809	0.194447262985	-0.0118729608718	0.0558553893695	0.208661072572	-0.0315379229061	0.142814270527	13.7121272576	19.8845040364	-12.3087936244
6	4.729050727	-0.82628212622	1.52843394023	2.1259264748	-0.671660677598	2.54515556722	-0.0453852463785	0.473466414757	0.249292377995	-0.0391826926111	-0.0781965313463	-0.694651035046	-0.11110754706	0.340505721344	0.126609311183	0.226496985844	-0.0263063990992	0.0495634795571	0.121003435874	-0.0571444725844	0.310040698646	24.472976495	35.4020894177	-4.36277977477
7	2.89852407618	-0.446109634337	0.201237218198	0.962848303429	0.376647865452	3.57223188956	-0.0957844980723	-0.404756870959	-0.123060491224	0.402483998619	0.108805550874	-0.573554075672	-0.0134352563405	0.192178975077	-0.0208379258846	0.282532134674	-0.0160333394509	-0.171881899671	0.231897886533	0.00755458506233	0.454461934379	30.5364173594	24.5766267078	11.6769573513
8	2.19431926811	-0.449723396226	0.295674804936	1.96792848782	-0.110116786172	1.37303764102	-0.0138659826009	-0.218804769731	-0.0356440371612	0.408906008778	-0.042559416705	-0.82384483458	0.024144376051	0.169365716465	0.0496586022194	0.224805252396	-0.00816572197013	-0.0913615032512	0.217816634961	-0.0262222237895	0.388684259728	28.2222444617	31.5698558304	9.27208346167
9	5.56090999227	0.389272565944	-2.8958315709	2.52667766653	2.28202990686	3.97740848384	0.0855331646987	0.375570558667	0.159606759193	-0.510054962596	-0.0843655373402	0.213287726453	-0.267506017126	-0.172783269205	-0.00927222626848	0.317102505437	0.0308738389263	-0.0725863917095	0.203581956478	-0.0290733221954	0.108012442492	-5.50660354925	30.0018674205	-21.5008641272
10	1.60937966942	-0.057320050504	0.728563920263	1.25371316137	-0.166698152999	0.766967775084	-0.0110714318704	0.0441313303152	0.125253462626	0.0546403939417	-0.020219395202	0.0728070117485	-0.153220879324	0.0359373296292	0.0182841828941	0.151679582881	0.0199942240667	0.0263516043919	0.146505979953	-0.0516633886466	0.0970036725417	-5.8684126559	38.1822543663	2.42605926537
11	0.67187156121	-0.141305495002	-0.166298030078	1.83435018678	0.2900272712	1.11786308263	-0.00415751192321	0.00835726556096	-0.0147531449883	0.10909159848	0.0415978875847	0.165329273565	-0.109344537973	-0.0162929555153	-0.0230282183855	0.155390534268	0.000597809168269	0.0223384680249	0.166534451731	-0.0168634002772	0.117956714171	-6.30667120664	12.9972864327	3.73495321321
12	1.92460126733	-2.05627929081	0.816295190021	5.23947561418	-1.02918838237	0.657070933952	0.0344771527915	-0.0596687238269	-0.107646875143	-0.12560312244	0.0361635324299	0.470130944903	0.0940143228732	-0.127587327521	-0.0761501509245	0.140260884318	-0.0182871889708	0.0428051573803	0.180943854121	-0.0318280935287	0.169541651878	-19.3860538106	7.18718030676	5.933923292
13	0.298472518276	0.130369838225	0.113721771894	1.55581904546	0.109864645606	0.323253323945	0.0248450061255	-0.0975219520452	0.00128010336383	0.249494711374	-0.0764927676619	0.31361763518	0.00730954383041	-0.0418862499667	0.0471134479398	0.213960112294	-0.000598260896805	0.0716910677231	0.193939156849	-0.0311871594339	0.161782188426	-11.3891881902	19.8318180656	12.3653680397
14	4.05983228485	1.56653517114	1.96669333685	1.36423721604	0.766247878601	2.17298605906	-0.0511137366267	-0.180420424465	0.188397113949	0.0354197289653	-0.0460463915128	0.550226656344	-0.135903130672	-0.21841580736	0.140269079807	0.162693730328	0.0335184036817	0.00745560689102	0.178471636741	-0.0419235995564	0.35683895389	-22.228665053	35.1869488365	4.24747668919
15	3.79731015555	1.02350523869	-0.614330812711	1.67913484169	-1.094526023	4.83739661833	-0.0664791432604	0.394178698472	-0.271297840348	-0.474694186798	0.0747676650456	0.64990653386	0.396980491213	-0.334294701891	0.00250232963426	0.280843322985	0.0330969543011	-0.12743904897	0.217666126425	-0.07090283687	0.432505959129	-28.1543103798	24.6449549857	-11.6648521216
16	1.80983243123	0.813006911413	0.320377231363	2.10234987743	-0.484412762545	0.965577039468	0.0419725727451	0.157781001988	0.0304841084874	-0.355825656477	-0.0931871755231	0.670162467227	-0.0727086997383	-0.211710499624	0.0703316672057	0.159235059823	0.0204500911548	-0.0794330629664	0.225626233651	-0.0276870899922	0.378710067254	-26.0376401907	31.5026595313	-9.47927386686

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 97 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 98 through 170 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 171 through 219 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 220 through 302 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 303 through 342 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 343 through 377 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 378 through 419 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 27 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 28 through 97 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 98 through 170 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 171 through 219 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 220 through 302 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 303 through 342 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 343 through 377 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 378 through 420 )

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