PDB-4i8a: Alanine-glyoxylate aminotransferase variant S187F

ID or keywords:

Entry

Database: PDB / ID: 4i8a

Title

Alanine-glyoxylate aminotransferase variant S187F

Components

Serine-pyruvate aminotransferase

Keywords

TRANSFERASE /

aminotransferase / primary hyperoxaluria type 1 /

peroxisome

Function / homology

Function and homology information

oxalic acid secretion /

serine-pyruvate transaminase /

alanine-glyoxylate transaminase / glycine biosynthetic process, by transamination of glyoxylate / glyoxylate metabolic process /

serine-pyruvate transaminase activity / L-alanine catabolic process /

alanine-glyoxylate transaminase activity / glyoxylate catabolic process / L-serine metabolic process ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Fodor, K. / Oppici, E. / Williams, C. / Cellini, B. / Wilmanns, M.

Citation

Journal: Proteins / Year: 2013
Title: Crystal structure of the S187F variant of human liver alanine: Aminotransferase associated with primary hyperoxaluria type I and its functional implications.
Authors: Oppici, E. / Fodor, K. / Paiardini, A. / Williams, C. / Voltattorni, C.B. / Wilmanns, M. / Cellini, B.

History

Deposition	Dec 3, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 2013	Provider: repository / Type: Initial release
Revision 1.1	Aug 7, 2013	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4i8a.cif.gz	578.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4i8a.ent.gz	481.7 KB	Display	PDB format
PDBx/mmJSON format	4i8a.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/i8/4i8a ftp://data.pdbj.org/pub/pdb/validation_reports/i8/4i8a	HTTPS FTP

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Related structure data

Related structure data	1h0cS 1jo4 S: Starting model for refinement
Similar structure data	5luc-1 5ofy-1 4cbs-1 5hhy-d 1j04-2 4cbr-1 6rv0-1 5luc-4 5kp5-1 5luc-3 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Serine-pyruvate aminotransferase

B: Serine-pyruvate aminotransferase

C: Serine-pyruvate aminotransferase

D: Serine-pyruvate aminotransferase

hetero molecules

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

1

A: Serine-pyruvate aminotransferase

B: Serine-pyruvate aminotransferase

hetero molecules

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

2

C: Serine-pyruvate aminotransferase

D: Serine-pyruvate aminotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.892, 101.564, 116.749
Angle α, β, γ (deg.)	90.00, 90.64, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

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

NCS domain segments:

Component-ID: 0 / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	LEU	LEU	A	A	6 - 389	8 - 391
2	1	LEU	LEU	B	B	6 - 389	8 - 391
1	2	LEU	LEU	A	A	6 - 389	8 - 391
2	2	LEU	LEU	C	C	6 - 389	8 - 391
1	3	LEU	LEU	A	A	6 - 389	8 - 391
2	3	LEU	LEU	D	D	6 - 389	8 - 391
1	4	LEU	LEU	B	B	6 - 389	8 - 391
2	4	LEU	LEU	C	C	6 - 389	8 - 391
1	5	LYS	LYS	B	B	5 - 390	7 - 392
2	5	LYS	LYS	D	D	5 - 390	7 - 392
1	6	LEU	LEU	C	C	6 - 389	8 - 391
2	6	LEU	LEU	D	D	6 - 389	8 - 391

NCS ensembles :

ID
1
2
3
4
5
6

#1: Protein	Serine-pyruvate aminotransferase / SPT / Alanine-glyoxylate aminotransferase / AGT Mass: 43479.180 Da / Num. of mol.: 4 / Mutation: S187F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: P21549, serine-pyruvate transaminase, alanine-glyoxylate transaminase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃

#1: Protein

Serine-pyruvate aminotransferase / SPT / Alanine-glyoxylate aminotransferase / AGT

Mass: 43479.180 Da / Num. of mol.: 4 / Mutation: S187F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Homo sapiens (human) / Gene: AGXT, AGT1, SPAT / Plasmid: pETM11 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P21549,

serine-pyruvate transaminase,

alanine-glyoxylate transaminase

#2: Chemical

ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL /

Glycerol

Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C₃H₈O₃

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.26 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 0.1 M LiSO4, 23 % [w/w] PEG4000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.812 Å
Detector	Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 26, 2011
Radiation	Monochromator: horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.812 Å / Relative weight: 1
Reflection	Resolution: 2.62→20.09 Å / Num. obs: 53733 / % possible obs: 96.7 % / Observed criterion σ(I): 3 / Redundancy: 3.2 % / B_iso Wilson estimate: 57.9 Å² / R_merge(I) obs: 0.195 / Net I/σ(I): 4.5

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Processing

Software

Name	Version	Classification
DNA		data collection
PHASER		phasing
REFMAC	5.7.0029	refinement
XDS		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H0C

1h0c

Resolution: 2.9→18.07 Å / Cor.coef. F_o:F_c: 0.848 / Cor.coef. F_o:F_c free: 0.824 / SU B: 46.974 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(I): 1.9 / ESU R Free: 0.459 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27813	2041	5 %	RANDOM
R_work	0.25136	-	-	-
obs	0.25273	38503	98.81 %	-
all	-	40642	-	-

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: 30.292 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	3.93 Å²	0 Å²	6.48 Å²
2-	-	-4.05 Å²	0 Å²
3-	-	-	0.04 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→18.07 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11834	0	78	0	11912

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	12202
X-RAY DIFFRACTION	r_bond_other_d	0.005	0.02	11730
X-RAY DIFFRACTION	r_angle_refined_deg	1.466	1.989	16578
X-RAY DIFFRACTION	r_angle_other_deg	1.031	3	27001
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.918	5	1544
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	38.201	23.729	472
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.045	15	1987
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.996	15	67
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	1854
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	13666
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	2656
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

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	23510	0.05
1	2	B	23510	0.05
2	1	A	23590	0.04
2	2	C	23590	0.04
3	1	A	23391	0.05
3	2	D	23391	0.05
4	1	B	23700	0.05
4	2	C	23700	0.05
5	1	B	23596	0.05
5	2	D	23596	0.05
6	1	C	23452	0.04
6	2	D	23452	0.04

LS refinement shell

Resolution: 2.9→2.975 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	147	-
R_work	0.315	2867	-
obs	-	-	99.83 %

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	0.08	0.0866	-0.0836	0.4209	-0.5992	0.9086	-0.0536	0.0791	0.0167	-0.0012	0.0762	0.0569	-0.0682	-0.0882	-0.0226	0.1005	0.014	-0.0783	0.248	-0.0185	0.1208	31.585	-9.6673	123.9006
2	1.7424	0.3977	0.5222	0.9413	-0.7475	1.0917	-0.0485	0.1055	-0.0421	-0.079	0.0482	-0.0025	0.0296	-0.0643	0.0003	0.0851	0.0304	-0.0822	0.2105	-0.0094	0.0938	10.7957	9.0217	124.29
3	1.0007	-0.405	-0.0461	2.6792	0.1631	0.4783	-0.0982	0.079	0.0133	-0.2003	0.0479	-0.052	0.0057	-0.0926	0.0502	0.1199	-0.0097	-0.0718	0.2789	0.0044	0.0769	25.8225	1.2213	117.1665
4	5.4525	0.1605	-7.6767	2.3803	1.7217	16.7132	-0.1279	0.1965	0.0108	-0.2246	0.1132	0.0482	-0.1149	-0.218	0.0147	0.0856	-0.0373	-0.0976	0.1241	-0.0035	0.1656	4.0483	-18.1845	127.4428
5	0.8591	0.3596	-0.3075	1.1536	-0.7937	0.5573	0.0029	-0.0985	-0.0986	0.0183	-0.0101	-0.035	0.0102	0.0025	0.0072	0.091	0.0048	-0.0901	0.2485	-0.0165	0.1021	8.0573	-14.617	139.3313
6	0.7412	0.3669	0.3466	0.7637	-0.2045	0.8009	0.0226	0.0807	-0.1642	-0.0513	0.0086	0.0231	-0.0342	0.0172	-0.0312	0.0704	0.01	-0.0903	0.2087	-0.0173	0.1433	34.2189	-12.9129	123.5976
7	0.4861	0.5215	-0.1236	0.84	-0.4664	0.4829	-0.0175	-0.0426	0.006	0.0113	0.0023	0.0013	-0.1057	0.0013	0.0152	0.1178	-0.0008	-0.0513	0.2092	-0.0353	0.1308	43.5288	12.9197	135.1859
8	0.431	0.4152	-0.0559	1.459	0.1886	0.1916	0.0154	-0.0123	-0.0195	0.0013	-0.0326	-0.0751	-0.0081	0.0595	0.0172	0.0651	0.0085	-0.0799	0.2281	-0.001	0.1067	40.986	5.6278	139.2775
9	1.2265	0.0724	-0.4046	5.2216	-5.0113	8.4618	-0.1443	-0.1085	0.1319	0.2195	-0.0231	-0.3126	-0.1304	0.554	0.1674	0.045	-0.0024	-0.0681	0.2893	-0.0337	0.1301	64.5568	-3.2251	127.104
10	0.5768	0.73	-0.2233	1.5643	0.1889	2.1732	-0.0027	-0.079	-0.0235	-0.0594	-0.0161	0.0245	-0.0101	0.0572	0.0188	0.0833	0.019	-0.0937	0.2322	-0.0007	0.1086	59.1239	-2.0069	116.1849
11	2.6382	-0.8697	1.4361	1.8023	-0.6456	2.3091	-0.188	-0.2143	-0.2471	0.3425	0.1424	-0.0161	-0.5091	-0.1543	0.0456	0.1808	-0.0179	-0.0187	0.2044	0.0019	0.1028	21.4695	33.5474	162.9494
12	0.5886	0.0491	0.1898	0.3041	0.3197	0.8976	0.0425	0.0364	-0.0738	0.0099	-0.0017	0.0366	-0.0095	-0.0846	-0.0409	0.0563	0.0008	-0.0736	0.1932	-0.0015	0.1261	-4.2031	15.9728	155.142
13	1.2119	0.1543	0.5721	0.4319	0.4619	0.6457	-0.0326	0.0592	0.0934	-0.0411	0.0186	-0.0478	-0.0691	-0.0034	0.014	0.0549	0.0244	-0.0681	0.2366	-0.0034	0.1178	-5.234	15.9518	161.4356
14	0.0532	-0.1167	0.2483	2.9352	-2.35	2.5066	0.0192	-0.0486	-0.0022	0.1347	0.0934	0.2732	-0.0571	-0.0965	-0.1125	0.0573	0.0041	-0.0453	0.2023	0.0151	0.1374	-4.695	28.9222	164.2961
15	1.9767	1.5928	-0.4049	1.2845	-0.3116	0.3739	-0.0842	0.1227	0.0218	-0.0621	0.0904	0.0225	0.103	0.0153	-0.0062	0.0693	0.0245	-0.0691	0.2197	0.0072	0.1262	8.8632	35.1069	139.9059
16	1.2059	-1.351	-0.945	4.0951	0.7124	0.7932	0.0608	0.0062	-0.003	0.037	-0.0624	0.1079	-0.078	-0.0267	0.0016	0.0749	0.0309	-0.0574	0.2686	0.0098	0.0671	-10.4252	33.7687	171.165
17	0.2912	0.0309	-0.1478	0.4742	0.3558	0.3787	-0.0164	-0.1087	-0.0682	0.0706	-0.0055	-0.0366	0.0542	0.1067	0.0219	0.0712	0.0043	-0.0886	0.2745	0.0075	0.1493	18.4713	11.2419	175.0334
18	0.4208	-0.387	-0.2394	1.3143	-0.2904	0.411	-0.041	-0.0856	0.0146	0.0596	0.0036	-0.0806	0.0084	0.0629	0.0374	0.0609	-0.0066	-0.0897	0.2976	-0.0085	0.1427	20.7267	15.5779	167.7801
19	7.9015	-2.6385	-1.2762	1.8718	-2.5666	9.2537	-0.1489	0.102	-0.8527	-0.1419	-0.0083	0.2728	0.6349	-0.068	0.1572	0.2817	-0.0169	-0.0428	0.2951	-0.0174	0.2787	30.0545	25.2917	185.3107
20	2.5533	-0.452	-0.7309	0.3825	0.4062	0.6424	-0.0539	-0.1458	0.0226	0.1006	0.0086	0.0294	0.0391	0.1431	0.0454	0.1309	-0.002	-0.0894	0.2562	0.0116	0.119	9.3208	21.5731	196.8024

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 80
2	X-RAY DIFFRACTION	2	A	81 - 188
3	X-RAY DIFFRACTION	3	A	189 - 285
4	X-RAY DIFFRACTION	4	A	286 - 308
5	X-RAY DIFFRACTION	5	A	309 - 392
6	X-RAY DIFFRACTION	6	B	5 - 55
7	X-RAY DIFFRACTION	7	B	56 - 146
8	X-RAY DIFFRACTION	8	B	147 - 285
9	X-RAY DIFFRACTION	9	B	286 - 310
10	X-RAY DIFFRACTION	10	B	311 - 390
11	X-RAY DIFFRACTION	11	C	6 - 32
12	X-RAY DIFFRACTION	12	C	33 - 184
13	X-RAY DIFFRACTION	13	C	185 - 250
14	X-RAY DIFFRACTION	14	C	251 - 297
15	X-RAY DIFFRACTION	15	C	298 - 390
16	X-RAY DIFFRACTION	16	D	5 - 23
17	X-RAY DIFFRACTION	17	D	24 - 174
18	X-RAY DIFFRACTION	18	D	175 - 282
19	X-RAY DIFFRACTION	19	D	283 - 289
20	X-RAY DIFFRACTION	20	D	290 - 390

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-Yorodumi

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Movie

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Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

-
Basic information

-
Structure visualization

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Downloads & links

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Download

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Validation report

-
Related structure data

-
Links

-
Assembly

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Components

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Experimental details

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Experiment

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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

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Yorodumi