PDB-6pk3: Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana

Basic information

• Entry: Database: PDB / ID: 6pk3
• Title: Alanine-glyoxylate aminotransferase 1 (AGT1) from Arabidopsis thaliana
• 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:

FORMIC ACID / PYRIDOXAL-5'-PHOSPHATE / Serine--glyoxylate aminotransferase

• Biological species: Arabidopsis thaliana (thale cress)
• Method: X-RAY DIFFRACTION / MIR / Resolution: 2.18 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	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 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)	89,090	6
Polymers	88,514	2
Non-polymers	576	4
Water	6,143	341

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, Apparent Molecular weight of 95,000 consistent with dimer
• 178 kDa, 4 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	178,179	12
Polymers	177,028	4
Non-polymers	1,152	8
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	23170 Å2
ΔGint	-121 kcal/mol
Surface area	48230 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
• 89.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	89,100	6
Polymers	88,514	2
Non-polymers	586	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	5980 Å2
ΔGint	-31 kcal/mol
Surface area	29670 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.
• 89.1 kDa, 2 polymers

Component details:

	Theoretical mass	Number of molelcules
Total (without water)	89,079	6
Polymers	88,514	2
Non-polymers	565	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	5760 Å2
ΔGint	-57 kcal/mol
Surface area	29990 Å2
Method	PISA

Unit cell

Length a, b, c (Å)	139.179, 62.289, 97.013
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-689- HOH
2	1	A-768- HOH
3	1	A-775- HOH
4	1	A-778- HOH
5	1	B-682- HOH
6	1	B-747- HOH
7	1	B-750- 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-FMT / FORMIC ACID

Details:

Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂

#4: Chemical

B-502 ChemComp-CL / CHLORIDE ION

Details:

Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

#5: Water

ChemComp-HOH / water

Details:

Mass: 18.015 Da / Num. of mol.: 341 / 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: 2.39 ų/Da / Density % sol: 48.57 % / Description: Clear
• Crystal grow: Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 ; Details: Protein: 11 mg/ml in 0.2 mM pyridoxal-phosphate, 10% glycerol, 100 mM Tris-HCl, pH 8.5. Precipitant: 4.1-4.2 M sodium formate. 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: 1.54 Å
• Detector: Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2002
• Radiation: Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
• Radiation wavelength: Wavelength: 1.54 Å / Relative weight: 1
• Reflection: Resolution: 2.18→22.6 Å / Num. obs: 41368 / % possible obs: 92.1 % / Redundancy: 5 % / B_iso Wilson estimate: 23.58 Ų / R_merge(I) obs: 0.077 / Net I/σ(I): 15.4

Reflection shell

Resolution (Å)	Rmerge(I) obs	Num. unique obs	Χ2	Diffraction-ID	% possible all
2.2-2.28	0.209	2127	1.12	1	48.2
2.28-2.37	0.193	3584	1.113	1	81.1
2.37-2.48	0.203	4187	1.143	1	94.5
2.48-2.61	0.192	4410	1.171	1	99.5
2.61-2.77	0.158	4431	1.158	1	99.9
2.77-2.99	0.127	4481	1.155	1	100
2.99-3.29	0.097	4447	1.128	1	99.9
3.29-3.76	0.07	4513	1.028	1	99.9
3.76-4.74	0.053	4540	0.968	1	99.9
4.74-30	0.042	4648	0.793	1	97.3

Processing

Software

Name	Version	Classification
PHENIX	1.15-2	refinement
PDB_EXTRACT	3.25	data extraction
SOLVE	2.02	phasing
SCALEPACK	1.6.1	data scaling
DENZO	0.95	data reduction

Refinement

Method to determine structure: MIR / Resolution: 2.18→22.6 Å / SU ML: 0.149 / Cross valid method: FREE R-VALUE / σ(F): 1 / Phase error: 16.2893

	Rfactor	Num. reflection	% reflection	Selection details
Rfree	0.1703	2789	7.02 %	random
Rwork	0.1393	-	-	-
obs	0.1415	39724	89.2 %	-

• Solvent computation: Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
• Displacement parameters: B_iso mean: 28.19 Ų

Refinement step

Cycle: LAST / Resolution: 2.18→22.6 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6195	0	36	341	6572

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0025	6460
X-RAY DIFFRACTION	f_angle_d	0.5424	8815
X-RAY DIFFRACTION	f_chiral_restr	0.0419	1007
X-RAY DIFFRACTION	f_plane_restr	0.0033	1125
X-RAY DIFFRACTION	f_dihedral_angle_d	10.6965	3824

LS refinement shell

Resolution (Å)	Rfactor Rfree	Num. reflection Rfree	Rfactor Rwork	Num. reflection Rwork	Refine-ID	% reflection obs (%)
2.18-2.22	0.2349	42	0.1797	709	X-RAY DIFFRACTION	34.01
2.22-2.26	0.1872	98	0.1848	1209	X-RAY DIFFRACTION	59.73
2.26-2.31	0.2091	117	0.1734	1459	X-RAY DIFFRACTION	71.34
2.31-2.35	0.2041	130	0.1676	1603	X-RAY DIFFRACTION	79.97
2.35-2.4	0.221	138	0.166	1741	X-RAY DIFFRACTION	85.56
2.4-2.46	0.1938	129	0.1604	1852	X-RAY DIFFRACTION	90.46
2.46-2.52	0.1905	152	0.1654	1908	X-RAY DIFFRACTION	93.76
2.52-2.59	0.1742	136	0.1634	1979	X-RAY DIFFRACTION	95.18
2.59-2.67	0.2079	138	0.1683	1946	X-RAY DIFFRACTION	95.16
2.67-2.75	0.2097	153	0.1555	1966	X-RAY DIFFRACTION	96.36
2.75-2.85	0.1896	157	0.1562	1974	X-RAY DIFFRACTION	96.25
2.85-2.96	0.1957	165	0.1578	2018	X-RAY DIFFRACTION	97.2
2.96-3.1	0.1997	136	0.1572	2013	X-RAY DIFFRACTION	97.77
3.1-3.26	0.1855	162	0.1518	1997	X-RAY DIFFRACTION	97.69
3.26-3.46	0.1489	144	0.1389	2081	X-RAY DIFFRACTION	98.32
3.46-3.73	0.1592	147	0.1235	2037	X-RAY DIFFRACTION	98.64
3.73-4.1	0.1467	153	0.1088	2080	X-RAY DIFFRACTION	99.16
4.1-4.69	0.1216	160	0.0979	2076	X-RAY DIFFRACTION	99.25
4.69-5.89	0.138	174	0.1194	2103	X-RAY DIFFRACTION	99.17
5.89-22.6	0.1743	158	0.1366	2184	X-RAY DIFFRACTION	96.86

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	3.34452470756	-2.71586956029	-0.0467352406612	2.38090537046	-0.0842768716324	0.745404963657	-0.00274203190186	-0.229513307696	0.150868882471	-0.0113033224649	0.142195420886	-0.138331644736	-0.110613155816	-0.0187917987696	-0.17588505655	0.187535262563	-0.0434130512164	0.00832756825479	0.165994366561	0.00915857047533	0.206387538022	-12.4216919741	2.79526409091	59.8768357463
2	4.76014546552	0.890383306154	1.8036055505	1.95185842334	0.950236534516	1.73574113049	0.0870661298213	0.205692348496	-0.461430621841	-0.0253299441056	0.00838951650886	-0.224185981269	0.168719173344	0.0699528909598	-0.11133270227	0.247077332614	-0.0158299460511	0.0178706116688	0.143028198401	-0.00583419022882	0.185318637304	2.94961747382	-13.2960649976	50.5520419532
3	1.26427684115	-0.109942765135	0.0148678432073	0.880314517202	0.302032986162	1.03639326724	-0.033018296902	0.455063696094	-0.0553545075633	-0.208106602523	0.0696172147979	0.00423262584506	-0.0247211105535	0.0101687320824	-0.0338563882571	0.218840759508	-0.0716379782545	-0.0191185879493	0.293640157516	-0.00825972392525	0.16535686255	-16.5188343793	-5.6651299731	29.0522612027
4	2.1483207207	-0.248200664631	-0.476914668417	0.616354746325	-1.00012931172	2.16902164744	0.0487967985295	0.455031340117	-0.505144824341	-0.0430411146814	0.222306303898	-0.041877457044	0.179469239511	0.179114021427	-0.247239432635	0.241102169215	-0.0674532905734	-0.0238491093001	0.31244688894	-0.113943430933	0.230798904872	-20.7933373348	-16.8685708592	27.1812877017
5	2.40587661835	-2.26607053951	-1.1688533088	4.50996810674	5.34877095764	8.86205653551	0.0261280254508	0.0954456376065	-0.308910749961	0.112655977794	0.0597028731054	0.137232691839	0.192982997982	0.0888793606648	-0.144555648277	0.199897302976	-0.0500134806159	-0.0172680652377	0.188997903319	-0.00196649741285	0.207825451923	-16.2590331717	-14.1419997116	40.6438593917
6	1.62840276167	0.2657438278	0.223814198286	0.618748977308	-0.0292661083709	1.18594890324	-0.0590346273032	0.286487193761	-0.203128224825	-0.0854436797023	0.0550134303367	-0.0688965749392	0.122544501054	0.0711510838409	0.000543205929766	0.216258277582	-0.0219575980981	0.0120621928036	0.166933152293	-0.0434446369362	0.236683139703	-1.35941068388	-11.3339015505	41.5625045591
7	1.01805821731	0.129395595683	-0.321517392536	0.903587902299	0.384261854418	2.28205818988	-0.0278649250686	0.20039531332	-0.186737500724	-0.0421634838272	0.0310644706898	0.156811339349	0.0408349053599	-0.12025470024	-0.0277946365683	0.184148434004	-0.0428077815357	-0.0207534750992	0.155744726319	0.00104047207799	0.193875186213	-30.6009259439	-5.28511036711	49.0708929671
8	2.37049966005	-1.03941125854	0.551927425454	1.96845802434	-0.320627791038	2.42204785757	-0.168206150612	0.247816243575	0.443010797861	-0.242189249845	0.101103719206	0.131554918414	-0.406127418927	-0.146237772301	0.0643784151831	0.231536869065	-0.00807977673034	-0.0357073995212	0.140852369759	0.062059370964	0.235893902417	-27.7969194607	13.7429411029	51.1342263304
9	1.76436672381	0.0776313938058	-0.531359661073	1.82697275841	-0.0243689136197	1.68413958986	-0.0242838146932	0.0434292688447	-0.0366565463786	-0.0397821442302	0.0383812712405	0.0697557166993	-0.0174383171097	-0.136396414787	-0.0397121410217	0.154796947987	-0.017264148325	-0.0277960803605	0.138332638405	0.00659320307943	0.158538249711	-28.6160150039	1.60892883797	57.0179972332
10	1.08854532876	-0.0840288568375	-0.237658813383	0.390707854354	0.0397301359972	0.675581766903	-0.0232374087521	-0.327056927148	0.143074991401	0.0809638128281	0.0708694617405	-0.0125817636092	-0.0650608191718	0.0457529355495	-0.0555186491436	0.180927187347	0.0566279852789	-0.00417027959612	0.200156330819	-0.0395178030555	0.166285132046	-8.38462153306	10.3851135825	91.4333660335
11	1.71702368169	0.199608823453	0.0533335480839	1.54776129197	0.0427722766963	1.6430375671	-0.0905130980436	-0.152844888778	-0.0380661196738	0.054755098127	0.0950667744189	0.0856360874487	0.00568953080711	-0.205095727375	-0.0138231615966	0.152618877606	0.0350121007505	0.0120695631084	0.168507583169	0.0192681900782	0.154033181227	-28.8458304602	3.46297461761	76.4134252627

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 3 through 27 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 28 through 55 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 56 through 155 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 156 through 175 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 176 through 198 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 199 through 270 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 271 through 307 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 308 through 330 )
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 331 through 401 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 2 through 270 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 271 through 401 )