PDB-5viu: Crystal Structure of Acetylornithine Aminotransferase from Elizab...

ID or keywords:

Entry

Database: PDB / ID: 5viu

Title

Crystal Structure of Acetylornithine Aminotransferase from Elizabethkingia anophelis

Components

Acetylornithine aminotransferase

Keywords

TRANSFERASE / SSGCID / Acetylornithine aminotransferase /

Elizabethkingia anophelis / argD / L-arginine biosynthesis /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

: /

ornithine aminotransferase activity /

ornithine aminotransferase / L-proline biosynthetic process /

pyridoxal phosphate binding
Similarity search - Function

Biological species

Elizabethkingia anophelis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Acetylornithine Aminotransferase from Elizabethkingia anophelis
Authors: Dranow, D.M. / Mayclin, S.J. / Lorimer, D.D. / Edwards, T.E.

History

Deposition	Apr 17, 2017	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 3, 2017	Provider: repository / Type: Initial release
Revision 1.1	Oct 4, 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

-
Download

PDBx/mmCIF format	5viu.cif.gz	332.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5viu.ent.gz	267.2 KB	Display	PDB format
PDBx/mmJSON format	5viu.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vi/5viu ftp://data.pdbj.org/pub/pdb/validation_reports/vi/5viu	HTTPS FTP

-
Related structure data

Related structure data	2oatS S: Starting model for refinement
Similar structure data	4jex-d 6us5-1 3tqx-d 6oia-1 6ueu-2 4ez9-2 4f4k-1 3qn3-3 5i92-2 1z6t-3 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: SSGCID-ElanA.01026.a

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Acetylornithine aminotransferase

B: Acetylornithine aminotransferase

hetero molecules

93.2 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, appears as a monomer by gel filtration

Unit cell

Length a, b, c (Å)	136.600, 77.470, 104.960
Angle α, β, γ (deg.)	90.000, 129.460, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Acetylornithine aminotransferase / ACOAT Mass: 46099.469 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia anophelis (bacteria) / Gene: argD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: A0A077E919, acetylornithine transaminase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₈O₇
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.33 Å³/Da / Density % sol: 47.1 %
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop Details: ElanA.01026.a.B1.PW37983 at 19.6 mg/ml, incubated with 3 mM ornithine and alpha-ketoglutaric acid and mixed 1:1 with an equal volume JCSG+(a3): 20% (w/v) PEG-3350, 200 mM ammonium citrate ...Details: ElanA.01026.a.B1.PW37983 at 19.6 mg/ml, incubated with 3 mM ornithine and alpha-ketoglutaric acid and mixed 1:1 with an equal volume JCSG+(a3): 20% (w/v) PEG-3350, 200 mM ammonium citrate dibasic, cryoprotected with 20% ethylene glycol

Crystal

Density Matthews: 2.33 Å³/Da / Density % sol: 47.1 %

Crystal grow

Temperature: 290 K / Method: vapor diffusion, sitting drop
Details: ElanA.01026.a.B1.PW37983 at 19.6 mg/ml, incubated with 3 mM ornithine and alpha-ketoglutaric acid and mixed 1:1 with an equal volume JCSG+(a3): 20% (w/v) PEG-3350, 200 mM ammonium citrate ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 22, 2017 / Details: Beryllium Lenses

Radiation

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

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.65→42.354 Å / Num. obs: 101355 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 3.792 % / B_iso Wilson estimate: 20.69 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.037 / R_rim(I) all: 0.043 / Χ²: 1.013 / Net I/σ(I): 20.68 / Num. measured all: 384308 / Scaling rejects: 6

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
1.65-1.69	3.761	0.514	2.52	7472	0.862	0.601	99.5
1.69-1.74	3.768	0.401	3.23	7263	0.905	0.468	99.8
1.74-1.79	3.779	0.313	4.17	7101	0.942	0.366	99.6
1.79-1.84	3.781	0.233	5.55	6884	0.965	0.273	99.6
1.84-1.91	3.791	0.185	6.97	6670	0.976	0.216	99.6
1.91-1.97	3.798	0.146	8.88	6422	0.984	0.171	99.5
1.97-2.05	3.793	0.108	11.71	6254	0.991	0.126	99.7
2.05-2.13	3.8	0.083	15.08	6015	0.994	0.097	99.6
2.13-2.22	3.806	0.065	18.76	5732	0.996	0.075	99.5
2.22-2.33	3.806	0.054	22.12	5513	0.997	0.063	99.5
2.33-2.46	3.81	0.047	25.29	5234	0.998	0.055	99.4
2.46-2.61	3.813	0.04	29.12	4972	0.998	0.047	99.6
2.61-2.79	3.813	0.035	33.3	4662	0.998	0.04	99.3
2.79-3.01	3.815	0.028	38.77	4332	0.999	0.033	99.4
3.01-3.3	3.825	0.024	44.47	3998	0.999	0.028	99.4
3.3-3.69	3.821	0.022	50.87	3627	0.999	0.025	99.2
3.69-4.26	3.811	0.019	55.87	3201	0.999	0.022	99.2
4.26-5.22	3.795	0.018	57.98	2728	0.999	0.021	98.8
5.22-7.38	3.752	0.019	56.8	2099	0.999	0.022	98.8
7.38-42.354	3.51	0.018	59.5	1176	0.999	0.022	96.1

-
Phasing

Phasing	Method: molecular replacement

-
Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHENIX		refinement
PDB_EXTRACT	3.22	data extraction
XDS		data reduction
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2OAT

2oat

Resolution: 1.65→42.354 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.99

	R_factor	Num. reflection	% reflection
R_free	0.1801	1923	1.9 %
R_work	0.1553	-	-
obs	0.1558	101344	99.78 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 97.67 Å² / B_iso mean: 30.2083 Å² / B_iso min: 11.78 Å²

Refinement step

Cycle: final / Resolution: 1.65→42.354 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5911	0	67	723	6701
B_iso mean	-	-	45.96	40.74	-
Num. residues	-	-	-	-	784

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	6262
X-RAY DIFFRACTION	f_angle_d	0.806	8531
X-RAY DIFFRACTION	f_chiral_restr	0.055	990
X-RAY DIFFRACTION	f_plane_restr	0.005	1108
X-RAY DIFFRACTION	f_dihedral_angle_d	15.21	3844

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6499-1.6912	0.2682	138	0.2365	7053	7191	100
1.6912-1.7369	0.2815	137	0.2163	7070	7207	100
1.7369-1.788	0.2297	153	0.1971	7051	7204	100
1.788-1.8458	0.2119	134	0.18	7098	7232	100
1.8458-1.9117	0.1877	148	0.1739	7075	7223	100
1.9117-1.9883	0.1926	119	0.1743	7056	7175	100
1.9883-2.0788	0.1807	137	0.1568	7115	7252	100
2.0788-2.1883	0.1824	129	0.1519	7126	7255	100
2.1883-2.3254	0.1934	120	0.1495	7113	7233	100
2.3254-2.505	0.1791	124	0.1543	7083	7207	100
2.505-2.757	0.1637	116	0.1597	7138	7254	100
2.757-3.1559	0.186	151	0.1529	7109	7260	100
3.1559-3.9756	0.1612	160	0.1362	7109	7269	100
3.9756-42.3678	0.1655	157	0.1452	7225	7382	99

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	3.4083	-1.8033	-1.4007	1.3028	0.5605	2.3112	-0.2286	-0.0858	-0.4977	-0.0254	0.0346	0.2662	0.4243	0.0305	0.1479	0.3112	-0.0119	0.0915	0.1478	0.0214	0.2772	2.4034	-27.4022	27.1726
2	1.5839	0.1006	-0.8903	0.3772	0.0047	1.3208	-0.0171	0.1992	-0.0294	-0.1303	0.0084	-0.0119	-0.0331	-0.1563	0.0072	0.1772	-0.0023	-0.0201	0.1493	-0.0042	0.1374	3.1302	-4.6665	15.1339
3	1.5724	0.1404	0.3432	1.2161	0.8283	3.7269	0.0445	-0.1344	-0.1136	-0.0752	0.1677	-0.5289	0.2697	0.624	-0.1144	0.1911	0.0168	0.0504	0.2821	-0.0613	0.3571	27.1507	2.7359	28.0365
4	1.1226	-0.6722	-0.0099	1.6069	-0.5389	0.5967	0.0003	-0.2389	-0.6903	-0.0252	0.041	-0.1263	0.7811	0.2861	-0.0942	0.3986	0.0819	-0.0999	0.4191	-0.0177	0.4627	25.4851	-5.8606	35.8252
5	3.7847	0.2862	0.1737	1.8827	0.3559	2.8692	0.0171	-0.3578	-0.005	0.1622	0.1077	-0.3077	-0.0495	0.2719	-0.0877	0.1257	0.002	-0.0336	0.178	-0.0342	0.1882	18.9597	9.2614	37.1172
6	1.4668	0.3137	-0.0747	1.3553	0.6399	2.1033	0.0365	0.05	0.0445	-0.1475	0.0843	-0.1498	-0.1264	0.1027	-0.0978	0.1569	-0.0176	0.0111	0.0895	0.0104	0.141	10.7987	3.7242	19.5391
7	2.767	1.1991	-2.6091	4.5027	-2.6989	3.0015	0.2763	-0.0657	0.2416	0.408	0.1087	0.4571	-0.4482	-0.1872	-0.449	0.1678	0.0068	0.0261	0.1315	-0.0219	0.2074	-8.7909	3.6443	37.4908
8	1.1824	-0.0417	-0.3328	3.6364	-1.5348	3.7396	-0.0089	-0.1103	-0.0701	0.2759	-0.0272	0.0079	0.0235	0.1421	0.0228	0.1215	0.006	0.0071	0.1342	-0.0062	0.1182	-5.6204	-8.6009	39.6933
9	1.0785	-0.0211	-0.7592	0.5834	0.4006	2.6217	0.077	0.1558	0.0988	-0.1792	-0.0019	-0.039	-0.2616	-0.1205	-0.0586	0.1872	0.0301	0.0001	0.1606	0.0154	0.1299	14.6983	-5.116	-0.3532
10	1.8812	-0.6866	-0.6499	0.9344	0.1577	0.983	-0.1771	-0.2137	0.0021	0.0759	0.1272	-0.1644	0.14	0.1649	0.0488	0.2441	-0.0023	0.0078	0.1536	-0.0125	0.1985	22.9389	-24.9004	19.0064
11	1.2153	0.5609	-0.3837	2.5634	-0.7294	1.958	-0.0104	0.0629	-0.1825	-0.412	-0.2073	-0.6569	0.2246	0.2086	0.168	0.2609	0.0488	0.1053	0.1793	0.0236	0.3081	30.9783	-14.689	-7.4682

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 4 through 28 )	A	4 - 28
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 29 through 108 )	A	29 - 108
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 109 through 144 )	A	109 - 144
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 145 through 178 )	A	145 - 178
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 179 through 233 )	A	179 - 233
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 234 through 313 )	A	234 - 313
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 314 through 335 )	A	314 - 335
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 336 through 411 )	A	336 - 411
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 72 )	B	4 - 72
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 73 through 313 )	B	73 - 313
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 314 through 411 )	B	314 - 411

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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