PDB-8e9k: Crystal structure of wild-type E. coli aspartate aminotransferase...

ID or keywords:

Entry

Database: PDB / ID: 8e9k

Title

Crystal structure of wild-type E. coli aspartate aminotransferase bound to maleate at 278 K

Components

Aspartate aminotransferase

Keywords

TRANSFERASE / Enzyme / Designed Protein / Mutant Protein

Function / homology

Function and homology information

L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / L-phenylalanine biosynthetic process / aspartate transaminase / L-aspartate:2-oxoglutarate aminotransferase activity / pyridoxal phosphate binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.83 Å

Authors

Chica, R.A. / St-Jacques, A.D. / Rodriguez, J.M. / Thompson, M.C.

Funding support

Canada,

United States, 5items

Organization	Grant number	Country
Natural Sciences and Engineering Research Council (NSERC, Canada)	RGPIN-2016-04831	Canada
Ontario Early Researcher Awards	ER14-10-139	Canada
Canada Foundation for Innovation	26503	Canada
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM124149	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM124169	United States

Citation

Journal: Nat Commun / Year: 2023
Title: Computational remodeling of an enzyme conformational landscape for altered substrate selectivity.
Authors: St-Jacques, A.D. / Rodriguez, J.M. / Eason, M.G. / Foster, S.M. / Khan, S.T. / Damry, A.M. / Goto, N.K. / Thompson, M.C. / Chica, R.A.

History

Deposition	Aug 26, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 5, 2022	Provider: repository / Type: Initial release
Revision 1.1	Nov 2, 2022	Group: Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2	Oct 11, 2023	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.3	Oct 18, 2023	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8e9k.cif.gz	576.4 KB	Display	PDBx/mmCIF format
PDB format	pdb8e9k.ent.gz	401.2 KB	Display	PDB format
PDBx/mmJSON format	8e9k.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e9/8e9k ftp://data.pdbj.org/pub/pdb/validation_reports/e9/8e9k	HTTPS FTP

-
Related structure data

Related structure data	8e9cC 8e9dC 8e9jC 8e9lC 8e9mC 8e9nC 8e9oC 8e9pC 8e9qC 8e9rC 8e9sC 8e9tC 8e9uC 8e9vC 1x28S 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

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#259 - Jul 2021 Designed Proteins and Citizen Science similarity (1) #70 - Oct 2005 Designer Proteins similarity (1)

Deposited unit

A: Aspartate aminotransferase

B: Aspartate aminotransferase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	143.830, 143.830, 81.570
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: -x,-y,z+1/2

#1: Protein	Aspartate aminotransferase / AspAT / Transaminase A Mass: 44776.453 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: aspC, b0928, JW0911 / Production host: Escherichia coli (E. coli) / References: UniProt: P00509, aspartate transaminase
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Chemical	ChemComp-MAE / MALEIC ACID Mass: 116.072 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 386 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.72 Å³/Da / Density % sol: 54.78 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, ammonium sulfate, maleate, PEG 400

-
Data collection

Diffraction	Mean temperature: 278 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 1, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.83→62.16 Å / Num. obs: 84225 / % possible obs: 100 % / Redundancy: 10.5 % / B_iso Wilson estimate: 29.87 Å² / CC_1/2: 0.996 / R_merge(I) obs: 0.2 / Net I/σ(I): 6.5
Reflection shell	Resolution: 1.83→1.86 Å / R_merge(I) obs: 1.8 / Num. unique obs: 4169 / CC_1/2: 0.348

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1_3660	refinement
xia2		data reduction
DIALS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1X28

1x28

Resolution: 1.83→47.08 Å / SU ML: 0.2449 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.1461
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1832	8482	10.08 %
R_work	0.1528	75691	-
obs	0.1559	84173	99.86 %

Solvent computation

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

Displacement parameters

B_iso mean: 36.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.83→47.08 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6147	0	0	386	6533

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0052	6714
X-RAY DIFFRACTION	f_angle_d	0.8117	9182
X-RAY DIFFRACTION	f_chiral_restr	0.0455	1002
X-RAY DIFFRACTION	f_plane_restr	0.0049	1246
X-RAY DIFFRACTION	f_dihedral_angle_d	20.7608	2426

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 (%)
1.83-1.85	0.3903	268	0.3478	2423	X-RAY DIFFRACTION	96.76
1.85-1.88	0.3688	283	0.3351	2537	X-RAY DIFFRACTION	99.96
1.88-1.9	0.3358	282	0.3124	2520	X-RAY DIFFRACTION	100
1.9-1.92	0.3089	279	0.3042	2497	X-RAY DIFFRACTION	100
1.92-1.95	0.3051	283	0.2806	2523	X-RAY DIFFRACTION	100
1.95-1.97	0.2649	280	0.2632	2515	X-RAY DIFFRACTION	100
1.97-2	0.2988	281	0.2569	2504	X-RAY DIFFRACTION	100
2-2.03	0.2537	284	0.2367	2521	X-RAY DIFFRACTION	100
2.03-2.06	0.2411	279	0.2275	2489	X-RAY DIFFRACTION	99.96
2.06-2.1	0.2673	286	0.2145	2530	X-RAY DIFFRACTION	100
2.1-2.13	0.2236	282	0.2058	2527	X-RAY DIFFRACTION	100
2.13-2.17	0.2434	279	0.2095	2503	X-RAY DIFFRACTION	100
2.17-2.21	0.2361	289	0.1987	2531	X-RAY DIFFRACTION	100
2.21-2.26	0.2131	311	0.1749	2478	X-RAY DIFFRACTION	100
2.26-2.31	0.2084	294	0.1671	2486	X-RAY DIFFRACTION	100
2.31-2.36	0.2056	253	0.1635	2602	X-RAY DIFFRACTION	100
2.36-2.42	0.1827	258	0.1574	2514	X-RAY DIFFRACTION	100
2.42-2.49	0.1674	286	0.1485	2505	X-RAY DIFFRACTION	100
2.49-2.56	0.1986	281	0.1574	2544	X-RAY DIFFRACTION	100
2.56-2.64	0.2004	274	0.1487	2522	X-RAY DIFFRACTION	99.96
2.64-2.74	0.1963	295	0.1466	2511	X-RAY DIFFRACTION	100
2.74-2.85	0.193	282	0.1509	2522	X-RAY DIFFRACTION	100
2.85-2.98	0.1958	292	0.1445	2530	X-RAY DIFFRACTION	100
2.98-3.13	0.1873	314	0.1452	2512	X-RAY DIFFRACTION	100
3.13-3.33	0.1827	293	0.1411	2510	X-RAY DIFFRACTION	100
3.33-3.59	0.1512	266	0.1256	2564	X-RAY DIFFRACTION	100
3.59-3.95	0.1313	285	0.1058	2549	X-RAY DIFFRACTION	100
3.95-4.52	0.1198	282	0.0923	2549	X-RAY DIFFRACTION	100
4.52-5.69	0.1227	282	0.1041	2560	X-RAY DIFFRACTION	100
5.7-47.08	0.1586	279	0.1467	2613	X-RAY DIFFRACTION	99.31

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	1.09805089837	-0.972595536323	-1.22836154559	2.31171060097	-0.353964001377	2.80460197925	-0.243485378856	0.264808573581	-0.279786375264	-0.0658239231568	-0.0272275726993	-0.760238022763	0.249901159719	0.274890700467	0.218593634277	0.365042263674	0.0226472117812	-0.00270671994059	0.443808983798	0.0859904368528	0.565090569359	53.3616578044	81.5813518352	-2.49200171231
2	1.58745286232	-1.81314944899	0.466941484351	3.29607716485	0.509575125949	2.26779449566	0.073495276853	0.140007284128	0.18835564526	-0.270219187261	0.134740870839	-0.243301498069	-0.292760415506	0.424957881497	-0.189809563045	0.446522134522	0.00720859407989	0.0683798785785	0.279360312339	-0.0176997802938	0.255202127763	38.3518989308	64.5979118635	-13.6151341771
3	0.542056508859	-0.226662227893	0.242568643091	1.20249614354	-0.470698251305	1.90971146254	0.0282104944143	-0.00479171288686	0.000614918026934	-0.0992995624988	0.0332390334896	0.192287350414	0.0261380416518	-0.171177879346	-0.0442708006176	0.220008333156	0.0396178045307	-0.0267554291286	0.218445745932	0.00707896822955	0.275876328293	23.4241719663	87.8179839203	-4.14015616228
4	0.384825373223	-0.210762281937	0.433320386575	1.31307196067	-0.546807002473	2.11916043235	0.0352138477446	-0.0899354702559	-0.0406083715463	0.0588456578521	0.0443265307756	0.149121053078	0.175996577369	-0.198575981062	-0.0801898369814	0.223768699334	0.00743443078127	-0.00940739116566	0.22456079109	0.00648421532699	0.252497462304	25.4051354087	79.4935766305	6.16785595742
5	2.75525442902	-2.25915661056	0.989130201079	4.57242444192	-0.915878060516	1.69354887718	0.023715945269	-0.213634372887	-0.0937644202136	-0.450802353773	0.146098205732	0.432869112077	0.311410746633	-0.152119151874	-0.113429492292	0.34760840722	-0.0452298397267	-0.0500738864349	0.232955977868	-0.00203244537346	0.237320813245	25.1327779654	60.0259882006	-8.84419635832
6	1.34426791948	-0.677194830121	-0.443334617801	2.84736314535	0.531611967995	2.79304275696	-0.0321469643694	-0.179926707828	0.0624554564384	0.236128927411	0.249152792389	-0.207647611725	-0.0164311838223	0.560798217996	-0.070192873457	0.375948252798	-0.00853982684516	-0.0236613223806	0.313020496968	-0.0259909147397	0.228920202352	39.3689173212	57.8105275536	-0.570244186541
7	1.7715318608	-1.01215590828	1.5327850887	2.30349277364	-0.795350472534	1.32782362305	-0.0988001079625	0.153376081231	0.247522139531	0.305512195012	0.287134507659	0.066869960001	-0.0835402317429	-0.409222722327	-0.238997983712	0.388082672099	0.0431626973914	0.0317415601358	0.348430794317	0.0414057713441	0.333406281695	22.9951361057	103.142375288	2.35836498219
8	0.211674405379	-0.353813850983	-0.00849924299027	1.77666136813	-0.497567203141	1.18070996951	0.0933045286136	0.104333464644	0.0206125288536	-0.358176966615	-0.151070534165	-0.0273041850085	0.239435690017	0.116614749747	0.0610494043112	0.311419069304	0.0534324005143	0.00294372001508	0.285710269531	0.0335270477272	0.259206620456	33.7884802816	94.046955255	-22.4572999821
9	1.62499083083	-0.279832347425	0.446238148026	1.74992743275	0.169430511729	0.91295991774	0.0108997151723	0.0832303364214	0.0975170666709	-0.0566392400785	-0.142971157181	-0.472849410562	0.217639740327	0.363879053745	0.108928546315	0.230050493374	0.0601209807798	0.006282192944	0.34377270355	0.110272425507	0.373312126412	50.6908194024	92.8052766811	-9.33623042845
10	1.38613677327	0.489408499006	-0.398824768587	2.28982329137	-0.0842557786535	0.933484005157	-0.123249678098	-0.136642415902	0.304138597726	0.384101466563	-0.144247234366	-0.366018534174	-0.430404803942	0.243114466601	0.277872657848	0.381248070647	-0.0696745918632	-0.155767151207	0.327410302924	0.0588767225118	0.476065940147	48.5383451422	111.871013828	-2.89115579131
11	3.23757719367	-0.289833549289	0.314383359843	1.02789500243	0.95861605684	1.00385113903	-0.0552200773465	-0.011868209437	0.279770190419	-0.0201634217837	-0.108899311353	-0.760182538321	-0.288373854542	0.533190440506	0.083863693706	0.316744015142	-0.103977058288	-0.0455747767033	0.468975550239	0.19736664826	0.658081022475	54.5875013211	112.5536262	-13.8230284495
12	0.650949936636	-0.269396501729	0.251566141461	1.18080341827	-0.487780023734	1.03216059225	0.0432644189355	0.103138953504	0.154350249336	-0.183951240688	-0.269925266252	-0.39868127002	0.0666335493406	0.394661337117	0.141987590419	0.225989428367	0.0544240791723	0.0148130476915	0.329018369841	0.106763304631	0.339525751746	47.7477081107	95.4745213999	-14.1651490196
13	1.2209387998	-2.99695361178	-0.359195850874	9.76809838885	1.31240122463	0.956272882361	0.156262416342	0.0849099009948	0.188600292575	-0.926956635628	-0.165111200153	-0.509979196077	0.0901398268602	0.141016572377	0.0310987568284	0.366028244538	0.0493617284073	0.0696850078885	0.35038249357	0.117235459777	0.339752767361	36.7520322671	110.674924745	-30.3377513819
14	2.29722716097	-0.90830201828	0.0605357817452	1.90012304442	-0.519662309659	2.01386531383	0.016046937691	-0.139165580154	0.197168277674	0.199072275248	-0.12150794191	-0.177725528836	-0.189234760154	-0.035934900422	0.0839347417334	0.259275991388	-0.0222909758195	-0.0353590439984	0.234875742111	0.0608541330302	0.286157858314	29.4144000346	120.931830763	-17.6025057041

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -2 through 22 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 23 through 46 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 47 through 127 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 128 through 300 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 301 through 332 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 333 through 396 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid -2 through 22 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 23 through 83 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 84 through 117 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 118 through 178 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 179 through 204 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 205 through 300 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 301 through 331 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 332 through 396 )

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi