PDB-3tvi: Crystal structure of Clostridium acetobutylicum aspartate kinase ...

ID or keywords:

Entry

Database: PDB / ID: 3tvi

Title

Crystal structure of Clostridium acetobutylicum aspartate kinase (CaAK): An important allosteric enzyme for industrial amino acids production

Components

Aspartokinase

Keywords

TRANSFERASE / Structural Genomics / ACT domains / Regulatory domains / Kinase / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC

Function / homology

Function and homology information

aspartate kinase / aspartate kinase activity / homoserine biosynthetic process / threonine biosynthetic process / lysine biosynthetic process via diaminopimelate / ATP binding / cytosol
Similarity search - Function

Biological species

Clostridium acetobutylicum (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 3 Å

Authors

Manjasetty, B.A. / Chance, M.R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)

Citation

Journal: Biotechnol Rep (Amst) / Year: 2014
Title: Crystal structure of Clostridium acetobutylicum Aspartate kinase (CaAK): An important allosteric enzyme for amino acids production.
Authors: Manjasetty, B.A. / Chance, M.R. / Burley, S.K. / Panjikar, S. / Almo, S.C.

History

Deposition	Sep 20, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 17, 2014	Group: Database references
Revision 1.2	Feb 10, 2021	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3tvi.cif.gz	1.9 MB	Display	PDBx/mmCIF format
PDB format	pdb3tvi.ent.gz	1.6 MB	Display	PDB format
PDBx/mmJSON format	3tvi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tv/3tvi ftp://data.pdbj.org/pub/pdb/validation_reports/tv/3tvi	HTTPS FTP

-
Related structure data

Similar structure data	6w51-1 6w51-4 5wnf-1 2c46-d 5tih-d 5wne-2 5kjr-d 4xak-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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
Other databases	TargetDB: NYSGXRC-6204B

Similar structure data

Other databases

TargetDB: NYSGXRC-6204B

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#61 - Jan 2005 Phenylalanine Hydroxylase similarity (3) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (3) #171 - Mar 2014 Neurotransmitter Transporters similarity (1)

Deposited unit

A: Aspartokinase

B: Aspartokinase

C: Aspartokinase

D: Aspartokinase

E: Aspartokinase

F: Aspartokinase

G: Aspartokinase

H: Aspartokinase

I: Aspartokinase

J: Aspartokinase

K: Aspartokinase

L: Aspartokinase

hetero molecules

596 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartokinase

B: Aspartokinase

hetero molecules

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

2

C: Aspartokinase

D: Aspartokinase

hetero molecules

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

3

E: Aspartokinase

F: Aspartokinase

hetero molecules

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

4

G: Aspartokinase

H: Aspartokinase

hetero molecules

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

5

I: Aspartokinase

J: Aspartokinase

hetero molecules

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

6

K: Aspartokinase

L: Aspartokinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	109.041, 274.217, 114.041
Angle α, β, γ (deg.)	90.00, 113.69, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Details

Six dimers

#1: Protein	Aspartokinase Mass: 49548.191 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C0278 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97MC0, aspartate kinase
#2: Chemical	ChemComp-ASP / ASPARTIC ACID Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C₄H₇NO₄
#3: Chemical	ChemComp-LYS / LYSINE Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₅N₂O₂

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.63 Å³/Da / Density % sol: 53.18 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: PEG 3350, 100mM Tris, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	NSLS	X29A	1	0.9792
SYNCHROTRON	NSLS	X3A	2	0.9792

Detector

Type	ID	Detector	Date	Details
ADSC QUANTUM 315r	1	CCD	Jun 21, 2007	mirrors
MAR CCD 165 mm	2	CCD	Jun 21, 2007	mirrors

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si(111)	SINGLE WAVELENGTH	M	x-ray	1
2	Si(111)	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9792	1
2		1

Reflection

Resolution: 3→50 Å / Num. obs: 217894 / % possible obs: 90 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / R_merge(I) obs: 0.086 / R_sym value: 0.086 / Net I/σ(I): 14

-
Processing

Software

Name	Version	Classification
CBASS		data collection
SHELXD		phasing
REFMAC	5.6.0116	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 3→44.16 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.896 / SU B: 50.934 / SU ML: 0.423 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.5 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FRIEDEL PAIRS WERE USED FOR PHASING.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27329	924	80 %	RANDOM
R_work	0.20622	-	-	-
obs	0.20678	111696	92.12 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 87.931 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.02 Å²	0 Å²	0.56 Å²
2-	-	0.11 Å²	0 Å²
3-	-	-	2.36 Å²

Refinement step

Cycle: LAST / Resolution: 3→44.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	38918	0	122	0	39040

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.02	39643
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	25918
X-RAY DIFFRACTION	r_angle_refined_deg	1.057	1.974	53658
X-RAY DIFFRACTION	r_angle_other_deg	0.841	3	63975
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.059	5	5175
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.736	25.862	1583
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.164	15	6487
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.014	15	93
X-RAY DIFFRACTION	r_chiral_restr	0.059	0.2	6281
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	44416
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	7393
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it
X-RAY DIFFRACTION	r_scbond_it
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3→3.078 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.334	67	-
R_work	0.306	7200	-
obs	-	-	81.35 %

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	1.0197	0.1781	-1.4697	0.3929	-0.353	2.7605	0.1426	-0.1691	0.0383	0.0241	0.0404	-0.1218	-0.2495	0.0488	-0.183	0.2988	0.0151	-0.0537	0.1012	0.0353	0.2024	-20.9704	50.7665	-48.7531
2	1.1183	-0.3087	1.2912	0.309	-0.6108	2.1756	-0.0114	-0.2211	0.1079	-0.1215	-0.1011	-0.0555	-0.0151	0.0635	0.1124	0.2093	0.0421	-0.0342	0.3491	0.029	0.0859	-13.9763	32.9985	0.7042
3	0.9022	0.1504	-0.2883	0.3644	0.5978	2.4764	0.1572	0.0035	0.1311	-0.0245	0.1277	-0.1191	-0.4298	-0.0223	-0.2849	0.2858	0.0365	-0.0771	0.1229	-0.0376	0.1619	22.071	54.3318	-3.2489
4	1.3575	0.0541	1.5125	0.9286	0.4876	1.9268	-0.0039	0.1079	-0.0484	0.0846	0.0368	0.0757	-0.0601	0.1327	-0.033	0.2249	-0.0519	0.0202	0.2367	0.049	0.1266	16.9839	30.7943	-49.9424
5	0.9973	0.5091	-0.3219	0.9008	-0.2295	1.163	0.0157	0.3265	-0.0107	-0.0184	-0.0353	0.0707	-0.0249	-0.0149	0.0196	0.2326	-0.0129	-0.074	0.1889	-0.0556	0.1559	47.746	4.8793	-21.2303
6	1.0772	-0.0463	-0.6325	0.5918	0.1853	2.0633	-0.0137	0.1982	-0.312	-0.0358	-0.1079	0.0602	0.469	-0.5924	0.1215	0.2273	-0.2205	-0.0829	0.3018	-0.0312	0.2527	7.6599	-9.7688	10.401
7	1.7999	-0.6144	-0.2549	0.5981	0.0858	0.8138	0.0405	-0.1431	0.0525	0.0038	0.0399	-0.131	0.0671	-0.2804	-0.0804	0.214	-0.0552	-0.063	0.1648	0.0448	0.1772	30.9008	10.9741	36.1073
8	0.9947	-0.7148	-0.1862	0.757	0.3967	2.9179	0.0921	-0.0349	-0.0829	0.1324	0.0128	0.0783	0.4004	0.4225	-0.1049	0.2453	0.0356	-0.1354	0.0817	-0.0742	0.3796	66.4204	-17.2344	8.5258
9	1.1183	0.1003	1.3464	1.339	-0.5357	2.428	0.1454	0.0339	0.4004	-0.2059	0.0456	0.3427	0.1243	0.1131	-0.191	0.3054	0.0952	0.3286	0.1418	0.0233	0.8256	-0.5635	95.4031	-56.8382
10	2.8296	0.4242	-0.8833	0.5955	-0.4048	0.4493	-0.0503	0.2876	-0.3686	0.0248	0.031	-0.1156	-0.0729	-0.0631	0.0193	0.3058	-0.018	0.1424	0.0603	-0.15	0.4903	43.9661	79.5487	-36.8263
11	0.6894	0.4437	-0.2178	0.7832	0.9537	2.5385	-0.2503	0.1457	-0.046	-0.2018	-0.1596	0.1136	-0.0922	-0.6133	0.4099	0.4175	0.0899	0.0165	0.2674	-0.2148	0.3745	53.8337	103.029	-69.6974
12	2.9174	1.4014	-0.842	0.8621	-0.6835	2.057	-0.0044	0.6445	-0.269	-0.0422	0.3854	0.008	0.1842	0.1302	-0.381	0.4487	-0.0366	0.0781	0.2746	-0.1315	0.2474	14.925	77.684	-92.0062

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 142
2	X-RAY DIFFRACTION	1	A	145 - 239
3	X-RAY DIFFRACTION	1	A	245 - 296
4	X-RAY DIFFRACTION	1	A	297 - 372
5	X-RAY DIFFRACTION	1	A	373 - 437
6	X-RAY DIFFRACTION	2	B	1 - 142
7	X-RAY DIFFRACTION	2	B	145 - 239
8	X-RAY DIFFRACTION	2	B	245 - 296
9	X-RAY DIFFRACTION	2	B	297 - 372
10	X-RAY DIFFRACTION	2	B	373 - 438
11	X-RAY DIFFRACTION	3	C	1 - 142
12	X-RAY DIFFRACTION	3	C	145 - 239
13	X-RAY DIFFRACTION	3	C	245 - 296
14	X-RAY DIFFRACTION	3	C	297 - 372
15	X-RAY DIFFRACTION	3	C	373 - 437
16	X-RAY DIFFRACTION	4	D	1 - 142
17	X-RAY DIFFRACTION	4	D	145 - 239
18	X-RAY DIFFRACTION	4	D	245 - 296
19	X-RAY DIFFRACTION	4	D	297 - 372
20	X-RAY DIFFRACTION	4	D	373 - 437
21	X-RAY DIFFRACTION	5	E	1 - 142
22	X-RAY DIFFRACTION	5	E	145 - 239
23	X-RAY DIFFRACTION	5	E	245 - 296
24	X-RAY DIFFRACTION	5	E	297 - 372
25	X-RAY DIFFRACTION	5	E	373 - 439
26	X-RAY DIFFRACTION	6	F	3 - 142
27	X-RAY DIFFRACTION	6	F	145 - 239
28	X-RAY DIFFRACTION	6	F	245 - 296
29	X-RAY DIFFRACTION	6	F	297 - 372
30	X-RAY DIFFRACTION	6	F	373 - 437
31	X-RAY DIFFRACTION	7	G	1 - 142
32	X-RAY DIFFRACTION	7	G	145 - 239
33	X-RAY DIFFRACTION	7	G	245 - 296
34	X-RAY DIFFRACTION	7	G	297 - 372
35	X-RAY DIFFRACTION	7	G	373 - 437
36	X-RAY DIFFRACTION	8	H	3 - 142
37	X-RAY DIFFRACTION	8	H	145 - 239
38	X-RAY DIFFRACTION	8	H	245 - 296
39	X-RAY DIFFRACTION	8	H	297 - 372
40	X-RAY DIFFRACTION	8	H	373 - 437
41	X-RAY DIFFRACTION	9	I	3 - 142
42	X-RAY DIFFRACTION	9	I	145 - 239
43	X-RAY DIFFRACTION	9	I	245 - 296
44	X-RAY DIFFRACTION	9	I	297 - 372
45	X-RAY DIFFRACTION	9	I	373 - 437
46	X-RAY DIFFRACTION	10	J	3 - 142
47	X-RAY DIFFRACTION	10	J	145 - 239
48	X-RAY DIFFRACTION	10	J	245 - 296
49	X-RAY DIFFRACTION	10	J	297 - 372
50	X-RAY DIFFRACTION	10	J	373 - 437
51	X-RAY DIFFRACTION	11	K	3 - 142
52	X-RAY DIFFRACTION	11	K	145 - 239
53	X-RAY DIFFRACTION	11	K	245 - 296
54	X-RAY DIFFRACTION	11	K	297 - 372
55	X-RAY DIFFRACTION	11	K	373 - 437
56	X-RAY DIFFRACTION	12	L	3 - 142
57	X-RAY DIFFRACTION	12	L	145 - 239
58	X-RAY DIFFRACTION	12	L	245 - 296
59	X-RAY DIFFRACTION	12	L	297 - 372
60	X-RAY DIFFRACTION	12	L	373 - 437

-
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