PDB-6pk1: Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis tha...

Basic information

• Entry: Database: PDB / ID: 6pk1
• Title: Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana in presence of serine
• Components: Serine--glyoxylate aminotransferase
• Keywords: TRANSFERASE / photorespiration / serine-glyoxylate aminotransferase / PLP / peroxisomal enzyme

Function / homology

Function:

serine-glyoxylate transaminase / L-serine-glyoxylate transaminase activity / serine-pyruvate transaminase / alanine-glyoxylate transaminase / L-serine-pyruvate transaminase activity / alanine-glyoxylate transaminase activity / Transferases; Transferring nitrogenous groups; Transaminases / photorespiration / apoplast / chloroplast stroma / chloroplast / peroxisome / mRNA binding / mitochondrion / plasma membrane / cytosol

Domain/homology:

Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase

Component:

3-HYDROXYPYRUVIC ACID / PYRIDOXAL-5'-PHOSPHATE / Serine--glyoxylate aminotransferase

• Biological species: Arabidopsis thaliana (thale cress)
• Method: X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
• Authors: Liepman, A.H. / Saper, M.A.

Funding support

United States, 1items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	NIH-GM08353	United States

• Citation: Journal: Front Plant Sci / Year: 2019; Title: Crystal Structure Of Photorespiratory Alanine:Glyoxylate Aminotransferase 1 (AGT1) FromArabidopsis thaliana.; Authors: Liepman, A.H. / Vijayalakshmi, J. / Peisach, D. / Hulsebus, B. / Olsen, L.J. / Saper, M.A.

History

Deposition	Jun 28, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 23, 2019	Provider: repository / Type: Initial release
Revision 1.1	Nov 20, 2019	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3	Oct 11, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Assembly

Deposited unit

A: Serine--glyoxylate aminotransferase

B: Serine--glyoxylate aminotransferase

hetero molecules

Summary:

• 89.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	89,112	5
Polymers	88,514	2
Non-polymers	598	3
Water	7,602	422

1

A: Serine--glyoxylate aminotransferase

B: Serine--glyoxylate aminotransferase

hetero molecules

A: Serine--glyoxylate aminotransferase

B: Serine--glyoxylate aminotransferase

hetero molecules

Summary:

• defined by author&software
• Evidence: gel filtration, Molecular weight of 95,000 consistent with dimer
• 178 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	178,224	10
Polymers	177,028	4
Non-polymers	1,197	6
Water	72	4

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1

Calculated values:

Buried area	22640 Å2
ΔGint	-98 kcal/mol
Surface area	48880 Å2
Method	PISA

2

A: Serine--glyoxylate aminotransferase

hetero molecules

A: Serine--glyoxylate aminotransferase

hetero molecules

Summary:

• defined by author&software
• Evidence: gel filtration, Molecular weight of 95,000 consistent with dimer
• 89.2 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	89,216	6
Polymers	88,514	2
Non-polymers	702	4
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1

Calculated values:

Buried area	6220 Å2
ΔGint	-25 kcal/mol
Surface area	29550 Å2
Method	PISA

3

B: Serine--glyoxylate aminotransferase

hetero molecules

B: Serine--glyoxylate aminotransferase

hetero molecules

Summary:

• defined by author&software
• Evidence: No biochemical or physiological evidence of tetramer, but see citation.
• 89 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	89,008	4
Polymers	88,514	2
Non-polymers	494	2
Water	36	2

Symmetry operations:

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_555	-x,-y,z	1

Calculated values:

Buried area	5590 Å2
ΔGint	-32 kcal/mol
Surface area	30150 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	139.179, 62.376, 96.982
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	18
Space group name H-M	P21212
Space group name Hall	P22ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x+1/2,y+1/2,-z #4: -x,-y,z

Components on special symmetry positions

ID	Model	Components
1	1	A-690- HOH
2	1	A-802- HOH
3	1	A-806- HOH
4	1	A-811- HOH
5	1	B-665- HOH
6	1	B-785- HOH
7	1	B-790- HOH

Components

#1: Protein

A B Serine--glyoxylate aminotransferase / Alanine--glyoxylate aminotransferase / AGT / Asparagine aminotransferase / Serine--pyruvate aminotransferase

Details:

Mass: 44256.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AGT1, At2g13360, F14O4.7 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q56YA5, serine-glyoxylate transaminase, alanine-glyoxylate transaminase, Transferases; Transferring nitrogenous groups; Transaminases, serine-pyruvate transaminase

#2: Chemical

A-501 B-501 ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate

Details:

Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P

#3: Chemical

A-502 ChemComp-3PY / 3-HYDROXYPYRUVIC ACID

Details:

Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₄O₄

#4: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 422 / Source method: isolated from a natural source / Formula: H₂O

• Has ligand of interest: N

Experimental details

Experiment

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

Sample preparation

• Crystal: Density Matthews: 2.4 ų/Da / Density % sol: 48.67 % / Description: Greenish-yellow
• Crystal grow: Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 ; Details: Protein: 11 mg/ml in 20 mM serine, 0.2 mM pyridoxal-phosphate, 10% glycerol, 100 mM Tris-HCl, pH 8.5. Precipitant: 4.1-4.2 M sodium formate, 20 mM serine. One microliter protein + 1 microliter precipitant equilibrated against precipitant.

Data collection

• Diffraction: Mean temperature: 295 K / Serial crystal experiment: N
• Diffraction source: Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 Å
• Detector: Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 22, 2001
• Radiation: Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.5418 Å / Relative weight: 1
• Reflection: Resolution: 2.1→22.16 Å / Num. all: 236629 / Num. obs: 45371 / % possible obs: 90.5 % / Redundancy: 5 % / B_iso Wilson estimate: 19.62 Ų / CC_1/2: 0.99 / R_merge(I) obs: 0.1 / R_pim(I) all: 0.04 / R_rim(I) all: 0.11 / Net I/av σ(I): 16 / Net I/σ(I): 16

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Rmerge(I) obs	Num. unique obs	CC1/2	Rpim(I) all	Rrim(I) all	Χ2	% possible all
2.1-2.14	2.3	0.263	1230	0.903	0.178	0.32	1.167	49.6
2.14-2.18	2.7	0.239	1557	0.939	0.147	0.283	1.26	62.9
2.18-2.22	3.1	0.236	1879	0.941	0.136	0.274	1.293	76.4
2.22-2.26	3.8	0.232	2147	0.951	0.121	0.264	1.331	87.2
2.26-2.31	4.6	0.199	2332	0.973	0.091	0.22	1.291	93.3
2.31-2.37	4.9	0.19	2359	0.977	0.087	0.21	1.297	96.4
2.37-2.42	5	0.189	2422	0.973	0.085	0.208	1.271	97.3
2.42-2.49	5.2	0.176	2426	0.978	0.08	0.194	1.309	98
2.49-2.56	5.3	0.165	2439	0.982	0.074	0.182	1.286	98.8
2.56-2.65	5.4	0.156	2453	0.983	0.071	0.172	1.246	98.7
2.65-2.74	5.4	0.142	2485	0.984	0.064	0.156	1.214	99.3
2.74-2.85	5.4	0.127	2467	0.987	0.057	0.14	1.141	99.2
2.85-2.98	5.5	0.117	2489	0.987	0.053	0.129	1.113	99.4
2.98-3.14	5.5	0.103	2497	0.989	0.046	0.113	1.04	99.4
3.14-3.33	5.6	0.096	2489	0.992	0.043	0.105	1.016	99.7
3.33-3.59	5.6	0.087	2510	0.992	0.039	0.096	0.991	99.8
3.59-3.95	5.6	0.08	2524	0.992	0.036	0.088	0.917	99.7
3.95-4.52	5.6	0.074	2537	0.992	0.034	0.082	0.843	99.6
4.52-5.7	5.5	0.068	2580	0.993	0.031	0.075	0.736	99.3
5.7-22.16	5.1	0.057	2622	0.989	0.029	0.064	0.923	94.4

Processing

Software

Name	Version	Classification
CNS	1.1	refinement
PHENIX	1.16rc1	refinement
PDB_EXTRACT	3.25	data extraction
DENZO	0.95	data reduction
SCALEPACK	1.6.1	data scaling

Refinement

Method to determine structure: FOURIER SYNTHESIS
Starting model: 6PK3

6pk3

Resolution: 2.1→22.16 Å / SU ML: 0.1602 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 15.3489 / Details: Used TLS with 15 groups

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.1661	3184	7.02 %	Random
Rwork	0.1151	-	-	-
obs	0.1187	45360	90.63 %	-

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / B_sol: 58.6 Ų / k_sol: 0.4 e/ų
• Displacement parameters: B_iso mean: 25.96 Ų

Refinement step

Cycle: LAST / Resolution: 2.1→22.16 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6190	0	39	422	6651

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0148	6412
X-RAY DIFFRACTION	f_angle_d	1.1319	8741
X-RAY DIFFRACTION	f_chiral_restr	0.074	1001
X-RAY DIFFRACTION	f_plane_restr	0.0083	1109
X-RAY DIFFRACTION	f_dihedral_angle_d	11.1837	3788

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.1-2.13	0.2671	63	0.1758	937	X-RAY DIFFRACTION	46.77
2.13-2.16	0.23	77	0.1552	1142	X-RAY DIFFRACTION	56.49
2.16-2.2	0.2286	112	0.1543	1347	X-RAY DIFFRACTION	68.34
2.2-2.24	0.2339	119	0.1386	1539	X-RAY DIFFRACTION	77.59
2.24-2.28	0.2146	137	0.1302	1732	X-RAY DIFFRACTION	87.3
2.28-2.32	0.1595	153	0.1219	1812	X-RAY DIFFRACTION	90.64
2.32-2.37	0.164	140	0.1221	1833	X-RAY DIFFRACTION	92.5
2.37-2.42	0.1955	147	0.1269	1887	X-RAY DIFFRACTION	94.12
2.42-2.48	0.1856	123	0.1225	1907	X-RAY DIFFRACTION	94.86
2.48-2.54	0.188	150	0.1225	1916	X-RAY DIFFRACTION	95.6
2.54-2.61	0.1974	148	0.1216	1932	X-RAY DIFFRACTION	96.39
2.61-2.68	0.1847	162	0.1235	1951	X-RAY DIFFRACTION	97.37
2.68-2.77	0.1688	140	0.1236	1959	X-RAY DIFFRACTION	97.27
2.77-2.87	0.1957	156	0.1263	1979	X-RAY DIFFRACTION	98.25
2.87-2.98	0.2224	122	0.1285	1985	X-RAY DIFFRACTION	97.77
2.98-3.12	0.1807	147	0.1293	2012	X-RAY DIFFRACTION	98.67
3.12-3.28	0.1967	143	0.1262	2014	X-RAY DIFFRACTION	98.99
3.28-3.49	0.1504	164	0.1118	1995	X-RAY DIFFRACTION	99.13
3.49-3.76	0.1614	144	0.0946	2019	X-RAY DIFFRACTION	98.99
3.76-4.13	0.1316	149	0.085	2051	X-RAY DIFFRACTION	99.5
4.13-4.73	0.1048	166	0.0785	2041	X-RAY DIFFRACTION	99.77
4.73-5.94	0.1346	159	0.0997	2063	X-RAY DIFFRACTION	99.46
5.94-22.16	0.1498	163	0.134	2123	X-RAY DIFFRACTION	96.42

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	1.580975936	-2.38037719809	-1.07382268043	4.37529929138	1.93558858832	3.01747622505	-0.0669592905496	0.0528779517826	0.243992552277	0.0610250131652	0.0685841664972	-0.234090639403	-0.336495369002	0.0493678980701	-0.00182185258281	0.133377370851	-0.0256449157935	-0.0141455185145	0.109474460372	0.0271309595882	0.176839280567	-14.9614374167	5.90233062564	58.5982132974
2	4.8589472523	0.781900254114	0.820180388646	2.02629045772	0.617918950429	1.35827356336	-0.044558631406	0.200123712271	-0.369938742877	-0.0922653922949	0.102970997268	-0.13980862895	0.0933151386734	0.0873156376281	-0.0582399589716	0.171894815667	-0.01932786505	0.00118397376238	0.0555857551886	0.0182483827208	0.113728640513	1.53728921991	-11.9857703747	52.5451060436
3	1.20726245714	0.386551589712	0.303860740758	0.782737667639	0.42665398163	0.813050914483	-0.0478214125102	0.518058126998	-0.154213618913	-0.181701043433	0.0759867789898	0.0352542597498	0.00626988997884	0.0327202826087	-0.0202633644605	0.206758546899	-0.073914300866	-0.0116477448511	0.310498362625	-0.0358727680558	0.15556700015	-17.3578407681	-7.64996580818	28.945610689
4	1.32464840643	-1.1743214254	0.0483824370621	4.48788374616	4.95776060761	8.24598144818	0.0340622452786	0.218041661712	-0.397807917164	0.148970149992	-0.0952103820883	0.0387547310717	0.322130737965	-0.149042148711	-0.00233811483936	0.136486869205	-0.049391079724	-0.0265148529878	0.15079756052	-0.0352806724433	0.201112966609	-16.3453385334	-14.1039362531	40.649559339
5	1.4683638163	0.144023939923	0.303325639981	0.381652640388	-0.110021685796	0.746049653807	-0.0611331574906	0.347235099009	-0.245624091101	-0.102292188038	0.0429513348377	-0.00945324335275	0.13940913681	0.0300289322958	0.0033803620503	0.176404542801	-0.0413831637512	0.01690082246	0.159627355451	-0.0573081367871	0.190043975639	-1.38148708627	-11.3366830684	41.5718062034
6	2.39069411406	-0.0641358274693	0.00361330914027	0.409352781606	0.172060315115	3.08800537281	-0.0214722389001	0.251666439251	-0.160148175399	-0.119181702244	0.00866547758405	0.121450614018	0.0724459837913	-0.146378377959	-0.0196648059851	0.142594650918	-0.0545692249458	-0.0177742905473	0.0972797249546	0.00317360882102	0.166475850135	-30.5853560729	-5.21430090151	49.0689468693
7	1.81873421341	-0.729050097403	0.35450598352	2.09309051619	-0.398072080077	2.39413578279	-0.105678382407	0.188151213265	0.337280182789	-0.183013875198	0.0448378776207	0.18417155252	-0.31886665191	-0.212290111642	0.0762954619784	0.190827258033	0.00870031098477	-0.0171534774831	0.13434627345	0.0764166684243	0.231670765233	-27.9242412842	13.8586856426	50.4415874225
8	1.97662684902	-0.165785606081	-0.266768353776	2.26132910087	-0.339136567366	1.59650697323	-0.0919467150735	0.0998658633922	-0.0180269736074	-0.0634492825951	0.100617114325	0.0884450283534	0.0130194386859	-0.133410430789	-0.0375688882704	0.117646638087	-0.019394319048	-0.0223260039422	0.114229127971	0.00469484546167	0.109834882353	-28.4362919116	2.00438989205	57.0405138009
9	1.3352956732	-0.20567200169	-0.0508080909265	0.379253818714	0.0450610328765	0.710464015735	-0.0471342381452	-0.388679527905	0.110075514895	0.070039462529	0.0872751578771	-0.0158411369569	-0.0108799794099	-0.0125156791451	-0.0580581144625	0.162815092072	0.0538656256905	-0.00193949424851	0.196305460227	-0.0281420324261	0.136679871485	-8.31457822094	6.3953952599	88.7556795994
10	0.494275822016	1.16769908993	1.54752613065	3.97164764014	3.50284747769	5.18298824235	0.0565407136246	-0.871876372728	0.215990808939	0.272839263897	0.192727576343	-0.0482338746337	-0.0583205366408	0.121495626457	-0.155311592667	0.239681988502	0.120717929542	0.0260290335512	0.509127724233	-0.0744742589801	0.188013337189	-19.4452113049	15.3083341164	109.513470058
11	1.17868444621	-0.0865550970193	-0.424235319639	0.445725162702	0.0390524069572	0.484888770839	-0.0124957070375	-0.387370081849	0.29654359723	0.0945190314032	0.065031987688	-0.0295324542056	-0.131657243191	0.0360528809027	-0.0665405026421	0.184935346897	0.0458774901125	-0.00842785519617	0.216412077691	-0.0780541765796	0.179721950849	-6.80710584063	13.6728752751	91.1966409791
12	1.86015490347	0.907814939108	0.43698010144	2.53571720655	0.00205049927683	2.28672561824	-0.127702883633	-0.329503799857	0.213769407303	0.0561118056869	0.100196024769	0.111024262441	-0.163156569069	-0.290140759455	-0.0232727181721	0.14504970304	0.0892632952168	0.0100141188355	0.155333089591	0.00412094750635	0.188620856975	-29.0421843992	10.8155254687	80.9963696862
13	3.18678364133	0.0767932123003	-1.55073599537	0.789423283201	0.402117260115	3.81992561331	-0.254742579967	-0.234793425524	-0.516417352198	0.105858728965	-0.00162779742932	0.245854819503	0.468166464777	-0.285096937001	0.222473778826	0.164886478194	-0.0131377425401	0.00493045992253	0.189598382981	0.0842506006458	0.253175481981	-29.9637230375	-8.43735164197	79.4266007932
14	1.99752788729	0.628504668663	0.243182054891	2.56674998058	-0.81630119533	3.54995963264	-0.089880899295	-0.208624903404	-0.153845094337	0.184412594324	0.115117735856	0.0408209740965	0.0536445235721	-0.204248975276	-0.0219810916629	0.104846947459	0.047621148727	0.0169188888046	0.114165943028	0.020323329914	0.142143961599	-26.4637804272	-1.34381990676	76.3506371534
15	3.35572831052	0.207308802841	-0.0296096063848	2.31072973581	0.261909069071	1.76235704349	0.000668412500444	-0.0314250664896	0.41457201302	0.104909580866	0.0447673409059	0.151115738132	-0.229726177696	-0.143525387467	-0.071849045496	0.164733518614	0.0400151472957	-0.0193113157596	0.100678109756	0.0174638259041	0.127125598428	-30.9937666988	10.8444789049	67.9585239574

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 21 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 22 through 55 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 175 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 176 through 198 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 199 through 270 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 271 through 307 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 308 through 329 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 330 through 401 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 3 through 122 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 123 through 144 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 145 through 270 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 271 through 307 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 308 through 329 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 330 through 372 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 373 through 401 )