PDB-3zzg: Crystal structure of the amino acid kinase domain from Saccharomy...

ID or keywords:

Entry

Database: PDB / ID: 3zzg

Title

Crystal structure of the amino acid kinase domain from Saccharomyces cerevisiae acetylglutamate kinase without ligands

Components

ACETYLGLUTAMATE KINASE

Keywords

TRANSFERASE / ARGININE BIOSYNTHESIS

Function / homology

Function and homology information

Urea cycle / ornithine biosynthetic process / N-acetyl-gamma-glutamyl-phosphate reductase / N-acetyl-gamma-glutamyl-phosphate reductase activity / acetylglutamate kinase / acetylglutamate kinase activity / L-arginine biosynthetic process / NADP+ binding / NAD binding / mitochondrial matrix ...
Similarity search - Function

Biological species

SACCHAROMYCES CEREVISIAE (brewer's yeast)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.95 Å

Authors

de Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V.

Citation

Journal: Plos One / Year: 2012
Title: Insight on an Arginine Synthesis Metabolon from the Tetrameric Structure of Yeast Acetylglutamate Kinase
Authors: De Cima, S. / Gil-Ortiz, F. / Crabeel, M. / Fita, I. / Rubio, V.

History

Deposition	Sep 1, 2011	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 2, 2012	Provider: repository / Type: Initial release
Revision 1.1	May 9, 2012	Group: Other
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

Remark 650

HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

Remark 700

SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3zzg.cif.gz	461.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3zzg.ent.gz	387.7 KB	Display	PDB format
PDBx/mmJSON format	3zzg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3zzg_validation.pdf.gz	456.7 KB	Display	wwPDB validaton report
Full document	3zzg_full_validation.pdf.gz	468.9 KB	Display
Data in XML	3zzg_validation.xml.gz	39 KB	Display
Data in CIF	3zzg_validation.cif.gz	52.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zz/3zzg ftp://data.pdbj.org/pub/pdb/validation_reports/zz/3zzg	HTTPS FTP

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Related structure data

Related structure data	3zzfSC 3zzhC 3zziC 4ab7C C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3zzf-d 3zzh-d 4tzw-d 4tzz-2 4tzp-2 4h26-d 4lck-2 3wf3-2 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

Deposited unit

A: ACETYLGLUTAMATE KINASE

B: ACETYLGLUTAMATE KINASE

C: ACETYLGLUTAMATE KINASE

D: ACETYLGLUTAMATE KINASE

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	68.086, 100.531, 188.740
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	C
1	2	B
2	2	D
1	3	A
2	3	C
1	4	B
2	4	D
1	5	A
2	5	C
1	6	B
2	6	D

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	3	A	58 - 98
2	1	1	3	C	58 - 98
1	1	2	3	B	58 - 92
2	1	2	3	D	58 - 92
1	1	3	3	A	99 - 272
2	1	3	3	C	99 - 272
1	1	4	3	B	99 - 272
2	1	4	3	D	99 - 272
1	1	5	3	A	273 - 360
2	1	5	3	C	273 - 360
1	1	6	3	B	273 - 360
2	1	6	3	D	273 - 360

NCS ensembles :

ID
1
2
3
4
5
6

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.3757, -0.06453, 0.9245), (-0.007006, -0.9973, -0.07246), (0.9267, -0.0337, 0.3743)	-18.32, 44.08, 14.01
2	given	(0.5614, -0.02194, -0.8272), (-0.01461, -0.9998, 0.0166), (-0.8274, 0.002763, -0.5616)	54.53, 38.52, 101.6
3	given	(-0.9762, 0.05225, -0.2103), (0.04651, 0.9984, 0.03212), (0.2116, 0.02157, -0.9771)	52.96, -1.424, 100.8

#1: Protein	ACETYLGLUTAMATE KINASE / N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ...N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ARG5\ / 6\ / MITOCHONDRIAL Mass: 34015.039 Da / Num. of mol.: 4 / Fragment: AMINO ACID KINASE DOMAIN, RESIDUES 58-356 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast) Strain: SIGMA 1278B / Plasmid: PYK6-AAK / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01217, acetylglutamate kinase

#1: Protein

ACETYLGLUTAMATE KINASE / N-ACETYLGLUTAMATE KINASE / N-ACETYL-L-GLUTAMATE 5-PHOSPHOTRANSFERASE / NAG KINASE / AGK / PROTEIN ...

Mass: 34015.039 Da / Num. of mol.: 4 / Fragment: AMINO ACID KINASE DOMAIN, RESIDUES 58-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: SIGMA 1278B / Plasmid: PYK6-AAK / Production host:

ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q01217, acetylglutamate kinase

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48 % / Description: NONE
Crystal grow	pH: 4.6 Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); PREVIOUS TO FREEZING, CRYSTAL WAS WASHED 6 HOURS IN ...Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); PREVIOUS TO FREEZING, CRYSTAL WAS WASHED 6 HOURS IN CRYSTALLIZATION BUFFER WITHOUT NAG. 25% GLYCEROL WAS USED AS CRYOPROTECTOR

Crystal

Density Matthews: 2.38 Å³/Da / Density % sol: 48 % / Description: NONE

Crystal grow

pH: 4.6
Details: PROTEIN WAS CRYSTALLIZED IN 50 MM NA-ACETATE, PH 4.6, 0.2 M NA-MALONATE AND 2% PEG 8000,, CONTAINING 24MM N-ACETYLGLUTAMATE (NAG); PREVIOUS TO FREEZING, CRYSTAL WAS WASHED 6 HOURS IN ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9393
Detector	Type: ADSC CCD / Detector: CCD / Date: Mar 3, 2011
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9393 Å / Relative weight: 1
Reflection	Resolution: 2.95→20 Å / Num. obs: 28023 / % possible obs: 99.8 % / Observed criterion σ(I): 2.1 / Redundancy: 6.4 % / B_iso Wilson estimate: 79.7 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.95→3.11 Å / Redundancy: 6.5 % / R_merge(I) obs: 0.37 / Mean I/σ(I) obs: 2.1 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZZF

3zzf

Resolution: 2.95→20 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.914 / SU B: 40.766 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.429 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24521	1398	5 %	RANDOM
R_work	0.21189	-	-	-
obs	0.21357	26458	99.75 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 81.447 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.3 Å²	0 Å²	0 Å²
2-	-	-4.04 Å²	0 Å²
3-	-	-	1.74 Å²

Refinement step

Cycle: LAST / Resolution: 2.95→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8978	0	0	0	8978

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	9106
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	6140
X-RAY DIFFRACTION	r_angle_refined_deg	1.078	1.979	12308
X-RAY DIFFRACTION	r_angle_other_deg	0.821	3	15102
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.749	5	1156
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.021	24.974	382
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.202	15	1682
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.96	15	48
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	1452
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	10028
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1704
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	0.408	1.5	5736
X-RAY DIFFRACTION	r_mcbond_other	0.051	1.5	2376
X-RAY DIFFRACTION	r_mcangle_it	0.774	2	9257
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.884	3	3370
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	1.585	4.5	3051
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	220	tight positional	0.02	0.05
1	2	C	220	tight positional	0.02	0.05
2	1	B	178	tight positional	0.03	0.05
2	2	D	178	tight positional	0.03	0.05
3	1	A	1023	tight positional	0.03	0.05
3	2	C	1023	tight positional	0.03	0.05
4	1	B	1023	tight positional	0.02	0.05
4	2	D	1023	tight positional	0.02	0.05
5	1	A	471	tight positional	0.02	0.05
5	2	C	471	tight positional	0.02	0.05
6	1	B	465	tight positional	0.02	0.05
6	2	D	465	tight positional	0.02	0.05
1	1	A	285	loose positional	0.02	5
1	2	C	285	loose positional	0.02	5
2	1	B	240	loose positional	0.03	5
2	2	D	240	loose positional	0.03	5
3	1	A	1194	loose positional	0.02	5
3	2	C	1194	loose positional	0.02	5
4	1	B	1182	loose positional	0.02	5
4	2	D	1182	loose positional	0.02	5
5	1	A	599	loose positional	0.02	5
5	2	C	599	loose positional	0.02	5
6	1	B	598	loose positional	0.05	5
6	2	D	598	loose positional	0.05	5
1	1	A	220	tight thermal	0.04	0.5
1	2	C	220	tight thermal	0.04	0.5
2	1	B	178	tight thermal	0.05	0.5
2	2	D	178	tight thermal	0.05	0.5
3	1	A	1023	tight thermal	0.04	0.5
3	2	C	1023	tight thermal	0.04	0.5
4	1	B	1023	tight thermal	0.04	0.5
4	2	D	1023	tight thermal	0.04	0.5
5	1	A	471	tight thermal	0.03	0.5
5	2	C	471	tight thermal	0.03	0.5
6	1	B	465	tight thermal	0.03	0.5
6	2	D	465	tight thermal	0.03	0.5
1	1	A	285	loose thermal	0.04	10
1	2	C	285	loose thermal	0.04	10
2	1	B	240	loose thermal	0.05	10
2	2	D	240	loose thermal	0.05	10
3	1	A	1194	loose thermal	0.04	10
3	2	C	1194	loose thermal	0.04	10
4	1	B	1182	loose thermal	0.05	10
4	2	D	1182	loose thermal	0.05	10
5	1	A	599	loose thermal	0.03	10
5	2	C	599	loose thermal	0.03	10
6	1	B	598	loose thermal	0.03	10
6	2	D	598	loose thermal	0.03	10

LS refinement shell

Resolution: 2.95→3.025 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.34	105	-
R_work	0.296	1873	-
obs	-	-	99.9 %

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	7.9376	-1.8746	-0.4366	14.8117	-0.7564	14.3711	0.0195	0.8233	-0.8455	-0.5104	0.3414	-0.1943	0.3735	0.2054	-0.361	0.2112	-0.0757	-0.0854	0.3515	-0.1787	0.4122	19.315	-2.161	47.191
2	10.1067	-4.3053	-2.298	13.3742	-0.1104	7.2515	-0.2824	0.3413	0.0162	0.0081	0.6351	0.3554	0.253	-0.6072	-0.3527	0.2144	-0.0164	-0.122	0.2566	-0.0285	0.1202	14.613	40.137	51.096
3	11.403	1.36	5.2814	5.7497	-1.9054	7.5494	-0.2917	-0.476	0.1967	0.421	0.2259	-0.2336	-0.2302	0.5097	0.0658	0.3218	0.0636	-0.1409	0.2916	-0.1672	0.2433	25.765	41.291	59.023
4	9.1728	0.3852	0.5651	9.5957	-2.3066	7.7999	-0.0467	-0.9921	-0.5573	0.3989	0.3658	0.3836	-0.0103	-0.6345	-0.3191	0.2865	0.0379	-0.0308	0.5107	0.0012	0.4741	19.66	-1.178	61.007
5	2.3942	0.0351	0.6575	4.4257	-0.4974	2.4863	-0.4512	0.4243	-0.352	-0.7793	0.4733	0.3175	0.277	-0.2728	-0.0221	0.5291	-0.4087	-0.0666	0.4563	-0.1031	0.2977	1.226	9.868	29.917
6	2.5272	0.7429	0.885	3.4052	0.2218	3.6884	-0.3258	0.4276	0.1924	-0.7233	0.427	0.1284	0.0926	-0.2888	-0.1012	0.456	-0.2658	-0.1115	0.4156	0.0748	0.2803	7.742	32.357	26.463
7	0.9003	0.4089	0.8809	3.3294	0.1517	5.6928	-0.1141	-0.3118	0.1986	0.751	0.1879	0.2919	-0.058	-0.0098	-0.0738	0.5285	0.2485	-0.059	0.4107	-0.1658	0.3165	29.81	29.565	83.84
8	1.8545	0.3975	0.6533	4.4663	1.2067	1.8851	-0.2512	-0.3555	-0.1362	0.8345	0.2829	-0.2334	0.1751	-0.0168	-0.0317	0.6097	0.3006	-0.0784	0.435	-0.0052	0.3022	36.139	6.986	80.351
9	17.6158	-0.0237	-10.7992	6.1715	0.2475	26.4539	-0.4329	1.3317	-1.7646	-1.1825	0.7485	0.1906	0.9792	-0.7382	-0.3156	0.493	-0.2982	-0.0654	0.2923	-0.2163	0.5276	-2.62	-15.176	27.01
10	22.4102	1.4937	3.3844	4.3316	-2.8179	19.2694	-0.5499	1.8844	2.7334	-0.5807	0.6973	1.138	-1.0652	-0.6619	-0.1474	0.3955	-0.1458	-0.3737	0.2775	0.4473	0.9731	6.782	57.497	23.541
11	32.0888	7.9709	5.6764	0.8979	4.482	39.2921	0.6836	-3.519	3.8001	-0.2594	-0.855	1.1449	-4.7532	-0.9671	0.1714	1.0934	0.1299	0.0276	0.5955	-0.992	1.4997	30.442	54.683	88.293
12	9.4746	-3.8073	-2.4928	7.1727	-6.0395	22.2266	-0.4009	-1.4754	-1.5995	0.462	0.1592	0.2361	0.8022	1.5086	0.2417	0.6991	0.3051	0.1996	0.3755	0.2904	0.5807	38.085	-18.21	83.662
13	5.0363	3.467	3.4248	10.4311	5.0871	20.7494	-0.358	0.4816	-1.0284	-1.1285	0.9963	-0.5231	-0.1507	0.8346	-0.6384	0.5682	-0.3135	0.0689	0.2526	-0.2364	0.5432	6.602	-7.239	29.788
14	16.1723	0.7702	5.969	9.4415	0.8447	7.221	-0.2236	0.007	1.0832	-0.5208	0.1992	1.4728	-0.6144	-0.5804	0.0245	0.3491	-0.0951	-0.117	0.1958	0.1334	0.5236	5.867	48.914	32.716
15	20.6691	6.9026	13.5664	7.6219	8.7041	18.9268	-0.2629	0.1888	0.8807	0.0354	0.375	-0.2252	-1.0517	0.46	-0.1121	0.5977	0.0935	-0.1696	0.118	-0.21	0.4119	33.175	46.564	79.214
16	6.9256	1.4293	-2.8964	4.6598	-2.2442	19.4345	-0.3907	-0.4069	-1.137	0.6362	0.3387	0.1902	0.8782	0.0207	0.0519	0.6091	0.24	0.1526	0.1315	0.1952	0.5601	29.943	-9.638	78.737

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	62 - 98
2	X-RAY DIFFRACTION	2	B	63 - 98
3	X-RAY DIFFRACTION	3	C	62 - 98
4	X-RAY DIFFRACTION	4	D	63 - 98
5	X-RAY DIFFRACTION	5	A	99 - 272
6	X-RAY DIFFRACTION	6	B	99 - 272
7	X-RAY DIFFRACTION	7	C	99 - 272
8	X-RAY DIFFRACTION	8	D	99 - 272
9	X-RAY DIFFRACTION	9	A	273 - 303
10	X-RAY DIFFRACTION	10	B	273 - 303
11	X-RAY DIFFRACTION	11	C	273 - 303
12	X-RAY DIFFRACTION	12	D	273 - 303
13	X-RAY DIFFRACTION	13	A	304 - 353
14	X-RAY DIFFRACTION	14	B	304 - 353
15	X-RAY DIFFRACTION	15	C	304 - 353
16	X-RAY DIFFRACTION	16	D	304 - 353

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