PDB-4rkd: Psychrophilic aromatic amino acids aminotransferase from Psychrob...

ID or keywords:

Entry

Database: PDB / ID: 4rkd

Title

Psychrophilic aromatic amino acids aminotransferase from Psychrobacter sp. B6 cocrystalized with aspartic acid

Components

Aromatic amino acid aminotransferase

Keywords

TRANSFERASE / AMINOTRANSFERASE / AROMATIC SUBSTRATES / PLP dependent ENZYME

Function / homology

Function and homology information

Transferases; Transferring nitrogenous groups; Transaminases / L-phenylalanine biosynthetic process from chorismate via phenylpyruvate / L-tyrosine-2-oxoglutarate transaminase activity / pyridoxal phosphate binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function

Biological species

Psychrobacter sp. B6 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.76 Å

Authors

Bujacz, A. / Rutkiewicz-Krotewicz, M. / Bujacz, G. / Nowakowska-Sapota, K. / Turkiewicz, M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Crystal structure and enzymatic properties of a broad substrate-specificity psychrophilic aminotransferase from the Antarctic soil bacterium Psychrobacter sp. B6.
Authors: Bujacz, A. / Rutkiewicz-Krotewicz, M. / Nowakowska-Sapota, K. / Turkiewicz, M.

History

Deposition	Oct 12, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 11, 2015	Provider: repository / Type: Initial release
Revision 1.1	Mar 18, 2015	Group: Database references
Revision 1.2	Apr 15, 2015	Group: Database references
Revision 1.3	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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4rkd.cif.gz	1.2 MB	Display	PDBx/mmCIF format
PDB format	pdb4rkd.ent.gz	1 MB	Display	PDB format
PDBx/mmJSON format	4rkd.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4rkd_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	4rkd_full_validation.pdf.gz	1.5 MB	Display
Data in XML	4rkd_validation.xml.gz	127.3 KB	Display
Data in CIF	4rkd_validation.cif.gz	173.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rk/4rkd ftp://data.pdbj.org/pub/pdb/validation_reports/rk/4rkd	HTTPS FTP

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Related structure data

Related structure data	4rkcSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3tat-2 3asa-1 4rkc-d 2hp0-d 1bqd-d 3dyd-d 1ay4-d 1ix8-1 6l1o-d 4wp0-1 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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4rkcSC

S: Starting model for refinement

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Aromatic amino acid aminotransferase

B: Aromatic amino acid aminotransferase

C: Aromatic amino acid aminotransferase

D: Aromatic amino acid aminotransferase

E: Aromatic amino acid aminotransferase

F: Aromatic amino acid aminotransferase

G: Aromatic amino acid aminotransferase

H: Aromatic amino acid aminotransferase

hetero molecules

357 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aromatic amino acid aminotransferase

B: Aromatic amino acid aminotransferase

hetero molecules

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

2

C: Aromatic amino acid aminotransferase

D: Aromatic amino acid aminotransferase

hetero molecules

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

3

E: Aromatic amino acid aminotransferase

F: Aromatic amino acid aminotransferase

hetero molecules

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

4

G: Aromatic amino acid aminotransferase

H: Aromatic amino acid aminotransferase

hetero molecules

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

Unit cell

Length a, b, c (Å)	92.250, 103.230, 165.780
Angle α, β, γ (deg.)	90.00, 98.58, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 1 - 398 / Label seq-ID: 1 - 398

NCS ensembles :

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein	Aromatic amino acid aminotransferase Mass: 44199.203 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter sp. B6 (bacteria) / Strain: B6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS References: UniProt: C7E5X4, aromatic-amino-acid transaminase

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Non-polymers , 6 types, 834 molecules

#2: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#4: Chemical	ChemComp-KET / 2-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYLENE)-AMINO]-SUCCINIC ACID / PYRIDOXYLIDENE-ASPARTIC ACID-5-MONOPHOSPHATE Mass: 363.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₂H₁₆N₂O₉P
#5: Chemical	ChemComp-OAA / OXALOACETATE ION Mass: 131.064 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₃O₅
#6: Chemical	ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE Mass: 248.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₃N₂O₅P
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.21 Å³/Da / Density % sol: 44.28 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.2M (CH3COO)2Mg, 20% PEG3350, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2012 / Details: mirrors
Radiation	Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9184 Å / Relative weight: 1
Reflection	Resolution: 2.76→50 Å / Num. obs: 77222 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.27 % / R_merge(I) obs: 0.126 / Net I/σ(I): 7.66
Reflection shell	Resolution: 2.76→2.86 Å / Redundancy: 2.26 % / R_merge(I) obs: 0.517 / Mean I/σ(I) obs: 2.29 / Num. unique all: 7979 / R_sym value: 0.523 / % possible all: 98.6

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
MOLREP		phasing
REFMAC	5.7.0032	refinement
XDS		data reduction
XDS		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4RKC

4rkc

Resolution: 2.76→45.74 Å / Cor.coef. F_o:F_c: 0.954 / Cor.coef. F_o:F_c free: 0.93 / SU B: 23.356 / SU ML: 0.236 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22194	3862	5 %	RANDOM
R_work	0.17338	-	-	-
all	0.17578	-	-	-
obs	0.17578	73358	97.38 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 39.782 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.93 Å²	-0 Å²	0.24 Å²
2-	-	4.88 Å²	0 Å²
3-	-	-	-2.86 Å²

Refinement step

Cycle: LAST / Resolution: 2.76→45.74 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	24808	0	201	818	25827

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.017	0.019	25725
X-RAY DIFFRACTION	r_angle_refined_deg	2.043	1.973	34877
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.092	5	3214
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.993	24.339	1180
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	19.407	15	4271
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.46	15	150
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	3782
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	19774
X-RAY DIFFRACTION	r_mcbond_it	2.76	2.803	12775
X-RAY DIFFRACTION	r_mcangle_it	4.429	4.192	15968
X-RAY DIFFRACTION	r_scbond_it	3.355	2.98	12950
X-RAY DIFFRACTION	r_long_range_B_refined	8.318	23.274	41135

Refine LS restraints NCS

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

LS refinement shell

Resolution: 2.76→2.831 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.375	286	-
R_work	0.321	5415	-
obs	-	-	98.75 %

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	1.1578	-0.2036	0.4006	0.0502	-0.0542	0.1611	0.025	0.2481	0.0315	0.0411	-0.0614	0.0162	0.0489	0.0782	0.0364	0.2131	-0.0296	0.0344	0.0597	-0.0013	0.0575	88.4035	55.946	52.6441
2	0.5308	0.1218	0.1106	0.0837	0.0539	0.4117	-0.0066	-0.0354	0.1218	0.0057	-0.0317	-0.0447	0.1013	-0.1425	0.0383	0.0766	0.0007	-0.0006	0.1359	-0.0294	0.1431	66.0848	58.9084	61.1735
3	0.2582	0.5079	0.1186	1.2111	0.0704	0.8801	-0.1472	0.0339	0.0368	-0.2054	-0.019	0.0364	0.0413	0.0162	0.1662	0.1373	-0.0106	0.0239	0.0823	0.0216	0.1142	76.1352	54.2557	39.027
4	0.0706	-0.1577	0.059	0.3688	-0.172	0.2115	0.0039	0.0414	0.0397	0.0266	-0.078	-0.0728	-0.1158	-0.0684	0.0741	0.1316	0.0263	0.0341	0.1537	-0.09	0.1756	88.0964	72.6364	74.5269
5	0.4209	-0.0605	0.1337	0.0122	0.0055	0.6496	-0.0119	-0.0437	-0.0025	-0.0049	-0.0075	-0.0009	0.0608	-0.0233	0.0194	0.161	0.002	-0.0088	0.0347	-0.0037	0.1356	94.3526	50.1873	80.463
6	0.6237	-0.2168	-0.3249	0.5214	0.7426	1.1374	-0.0369	-0.0955	0.1433	0.0243	0.1222	0.0127	0.0589	0.2123	-0.0853	0.1234	0.0131	0.0012	0.0478	-0.0516	0.1705	99.4723	72.8539	89.2322
7	0.1202	-0.0002	0.2216	0.0021	-0.0014	0.4979	0.0422	-0.0797	-0.0063	-0.0129	-0.0022	0.0041	0.009	-0.0984	-0.04	0.1448	-0.0257	-0.0079	0.0968	-0.0047	0.0961	48.1138	56.3302	120.0284
8	0.0451	0.0418	0.061	0.2095	-0.1153	0.6022	0.0197	0.0666	0.0405	0.02	-0.0353	0.1532	0.0188	0.3616	0.0156	0.0126	0.0009	0.0197	0.283	0.0221	0.1294	70.493	59.344	111.4409
9	0.0992	-0.2704	0.2586	1.0886	-0.4843	1.331	-0.0168	0.0102	0.0586	0.0568	-0.1145	-0.0512	0.1243	0.0696	0.1313	0.0812	-0.042	-0.0106	0.1425	-0.0322	0.0834	60.3995	55.1229	133.6849
10	0.0639	-0.004	-0.1881	0.1838	-0.1332	0.7789	0.0257	-0.0608	0.0333	0.0831	0.0123	0.0816	-0.167	0.1966	-0.038	0.0713	-0.0388	-0.0137	0.1199	0.0066	0.1869	48.3385	72.2521	97.8477
11	0.1684	0.0726	0.0287	0.2394	-0.1433	0.6975	0.0026	-0.0266	0.0138	-0.0415	-0.0248	0.0328	0.0919	0.0226	0.0222	0.1595	0.019	-0.0227	0.0116	0.0034	0.1508	42.3757	49.8133	92.315
12	0.2765	0.1244	-0.1394	0.1824	-0.5128	1.7221	-0.0292	-0.0163	0.0578	-0.0333	0.0202	0.0335	0.0301	-0.0513	0.009	0.1561	0.0234	-0.0017	0.0222	0.0188	0.1563	37.0357	72.2172	83.1734
13	0.0686	-0.0176	0.1144	0.1167	-0.1268	0.2761	-0.0424	0.0354	0.0983	-0.027	-0.0473	0.0555	-0.0165	0.0747	0.0898	0.0546	-0.0571	-0.0187	0.1063	-0.0517	0.284	55.9388	25.6534	148.0033
14	0.2356	-0.1382	-0.0921	0.1387	-0.0426	0.2726	-0.0154	-0.0529	0.0247	-0.0544	0.0006	-0.026	0.0615	0.0142	0.0149	0.1379	-0.0004	0.0252	0.1107	-0.0301	0.1161	56.2519	2.9702	155.7513
15	0.0476	0.0594	-0.0201	0.4993	0.6284	2.1401	0.0321	0.0215	0.0489	0.0777	-0.0425	0.0693	0.0175	0.1335	0.0104	0.0735	-0.0473	0.0994	0.12	-0.0377	0.1452	67.0307	24.0515	162.6845
16	0.876	-0.0516	0.0441	0.0159	-0.0083	0.0264	0.0595	0.1421	0.0303	0.0374	-0.0304	0.0103	0.0286	0.051	-0.0291	0.2232	0.0101	-0.0131	0.1141	-0.0507	0.0662	51.619	7.5725	127.5015
17	0.5753	-0.1504	0.1277	0.1716	0.0873	0.1565	0.039	-0.0448	0.1226	0.0012	-0.0615	-0.0892	0.0203	-0.1159	0.0225	0.1255	-0.014	0.0287	0.1086	-0.0413	0.1365	31.2381	17.6661	135.3873
18	0.0846	0.1532	0.119	0.3543	0.4506	0.9183	0.0048	0.0191	0.0181	0.0251	0.001	0.0072	0.0255	-0.0639	-0.0058	0.1223	-0.0028	0.0249	0.0823	0.0186	0.1306	39.2865	8.352	113.8498
19	0.2863	-0.1812	0.1658	0.1857	-0.1131	0.1099	-0.0133	-0.0659	0.0164	-0.0322	0.0245	0.0015	-0.038	0.0118	-0.0112	0.1097	-0.1014	0.0525	0.1964	-0.0965	0.0484	32.3399	78.045	156.3445
20	0.5705	-0.1086	-0.2887	0.1066	0.2435	0.6273	-0.1354	-0.1419	-0.1083	-0.0081	0.0856	0.0444	0.0425	0.2298	0.0498	0.101	0.0538	-0.0057	0.184	0.0304	0.0907	32.996	55.1075	164.4393
21	0.0189	-0.0255	0.0405	0.9198	0.5861	1.1626	0.0293	-0.0494	0.0215	-0.0083	0.0622	-0.0225	0.0339	0.0791	-0.0916	0.0286	-0.0591	0.0311	0.2905	-0.1192	0.0634	43.4172	76.6871	171.2104
22	0.4699	-0.1906	0.1507	0.1005	-0.008	0.1858	0.0118	0.0662	-0.0557	-0.0331	0.026	0.0156	-0.006	0.1752	-0.0377	0.1481	-0.0373	0.0401	0.1872	-0.0333	0.0831	28.1983	59.5842	136.1482
23	0.2403	-0.0998	-0.0674	0.0912	0.1535	0.528	0.0375	-0.0386	0.0109	-0.0308	0.0291	-0.0272	-0.1032	-0.0638	-0.0666	0.1439	-0.0038	0.0416	0.072	-0	0.1261	7.7187	69.2939	144.0573
24	0.2006	0.4264	0.1795	0.9644	0.5087	0.8616	-0.0148	0.0032	-0.0001	-0.0064	0.0096	0.0617	-0.0221	0.0457	0.0053	0.1168	-0.0113	0.0106	0.0718	0.0119	0.1209	15.8914	60.1837	122.5341

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 66
2	X-RAY DIFFRACTION	2	A	67 - 287
3	X-RAY DIFFRACTION	3	A	288 - 398
4	X-RAY DIFFRACTION	4	B	1 - 66
5	X-RAY DIFFRACTION	5	B	67 - 287
6	X-RAY DIFFRACTION	6	B	288 - 398
7	X-RAY DIFFRACTION	7	C	1 - 66
8	X-RAY DIFFRACTION	8	C	67 - 287
9	X-RAY DIFFRACTION	9	C	288 - 398
10	X-RAY DIFFRACTION	10	D	1 - 66
11	X-RAY DIFFRACTION	11	D	67 - 287
12	X-RAY DIFFRACTION	12	D	288 - 398
13	X-RAY DIFFRACTION	13	E	1 - 66
14	X-RAY DIFFRACTION	14	E	67 - 287
15	X-RAY DIFFRACTION	15	E	288 - 398
16	X-RAY DIFFRACTION	16	F	1 - 66
17	X-RAY DIFFRACTION	17	F	67 - 287
18	X-RAY DIFFRACTION	18	F	288 - 398
19	X-RAY DIFFRACTION	19	G	1 - 66
20	X-RAY DIFFRACTION	20	G	67 - 287
21	X-RAY DIFFRACTION	21	G	288 - 398
22	X-RAY DIFFRACTION	22	H	1 - 66
23	X-RAY DIFFRACTION	23	H	67 - 287
24	X-RAY DIFFRACTION	24	H	288 - 398

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