PDB-3wwi: Crystal structure of the G136F mutant of the first R-stereoselect...

ID or keywords:

Entry

Database: PDB / ID: 3wwi

Title

Crystal structure of the G136F mutant of the first R-stereoselective -transaminase identified from Arthrobacter sp. KNK168 (FERM-BP-5228)

Components

(R)-amine transaminase

Keywords

TRANSFERASE / transaminase / amine-pyruvate aminotransferase / PYRIDOXAL-5'-PHOSPHATE / Multi-domain protein (alpha and beta) / Fold class IV PLP-dependent enzyme

Function / homology

Function and homology information

carboxylic acid biosynthetic process / catalytic activity
Similarity search - Function

Biological species

Arthrobacter sp. KNK168 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.27 Å

Authors

Guan, L.J. / Ohtsuka, J. / Miyakawa, T. / Zhi, Y. / Ito, N. / Yasohara, Y. / Tanokura, M.

Citation

Journal: Sci Rep / Year: 2015
Title: A new target region for changing the substrate specificity of amine transaminases.
Authors: Guan, L.J. / Ohtsuka, J. / Okai, M. / Miyakawa, T. / Mase, T. / Zhi, Y. / Hou, F. / Ito, N. / Iwasaki, A. / Yasohara, Y. / Tanokura, M.

History

Deposition	Jun 18, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Aug 19, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 21, 2018	Group: Data collection / Database references / Category: citation Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Jan 22, 2020	Group: Advisory / Database references / Derived calculations Category: pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms ...pdbx_distant_solvent_atoms / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item: _struct_ref_seq_dif.details / _struct_site.details ..._struct_ref_seq_dif.details / _struct_site.details / _struct_site.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3wwi.cif.gz	1.5 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	3wwi_validation.pdf.gz	533.9 KB	Display	wwPDB validaton report
Full document	3wwi_full_validation.pdf.gz	569.8 KB	Display
Data in XML	3wwi_validation.xml.gz	150.5 KB	Display
Data in CIF	3wwi_validation.cif.gz	210.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ww/3wwi ftp://data.pdbj.org/pub/pdb/validation_reports/ww/3wwi	HTTPS FTP

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Related structure data

Related structure data	3wwhC 3wwjC C: citing same article (ref.)
Similar structure data	6snl-3 4ce5-d 3wwj-4 3ht5-1 4cmd-d 2e8w-d 4dqn-1 3wwj-5 6bal-3 6fte-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) 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

3wwhC

3wwjC

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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (6)

Deposited unit

A: (R)-amine transaminase

B: (R)-amine transaminase

C: (R)-amine transaminase

D: (R)-amine transaminase

E: (R)-amine transaminase

F: (R)-amine transaminase

G: (R)-amine transaminase

H: (R)-amine transaminase

I: (R)-amine transaminase

J: (R)-amine transaminase

K: (R)-amine transaminase

L: (R)-amine transaminase

hetero molecules

441 kDa, 12 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: (R)-amine transaminase

B: (R)-amine transaminase

hetero molecules

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

2

C: (R)-amine transaminase

D: (R)-amine transaminase

hetero molecules

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

3

E: (R)-amine transaminase

L: (R)-amine transaminase

hetero molecules

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

4

F: (R)-amine transaminase

K: (R)-amine transaminase

hetero molecules

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

5

G: (R)-amine transaminase

J: (R)-amine transaminase

hetero molecules

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

6

H: (R)-amine transaminase

I: (R)-amine transaminase

hetero molecules

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

Unit cell

Length a, b, c (Å)	81.960, 134.280, 196.040
Angle α, β, γ (deg.)	90.00, 100.34, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	(R)-amine transaminase / R-stereoselective-transaminase Mass: 36542.945 Da / Num. of mol.: 12 / Mutation: G136F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter sp. KNK168 (bacteria) / Gene: TAS / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: F7J696, EC: 2.1.6.18
#2: Chemical	ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate Mass: 247.142 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₈H₁₀NO₆P
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1856 / 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: 2.42 Å³/Da / Density % sol: 49.18 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8 Details: 0.2M magnesium chloride, 0.1M HEPES-HCl, 16% PEG 3350, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2013
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.27→50 Å / Num. all: 193164 / Num. obs: 190871 / % possible obs: 98.8 % / Observed criterion σ(I): -3
Reflection shell	Resolution: 2.27→2.4 Å / % possible all: 95.9

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Processing

Software

Name	Version	Classification
XDS		data scaling
MOLREP		phasing
REFMAC	5.8.0071	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.27→40 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.946 / SU B: 14.346 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R: 0.312 / ESU R Free: 0.213 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.21791	9595	5 %	RANDOM
R_work	0.17097	-	-	-
obs	0.1733	181256	98.81 %	-

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: 43.991 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.06 Å²	-0 Å²	-0.92 Å²
2-	-	0.33 Å²	0 Å²
3-	-	-	-0.05 Å²

Refinement step

Cycle: LAST / Resolution: 2.27→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	30292	0	180	1856	32328

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	31228
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	29120
X-RAY DIFFRACTION	r_angle_refined_deg	1.455	1.962	42688
X-RAY DIFFRACTION	r_angle_other_deg	0.783	3	66884
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.029	5	3852
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.542	23.554	1452
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.675	15	4792
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.425	15	240
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	4776
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	35484
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	7140
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	1.226	2.172	15444
X-RAY DIFFRACTION	r_mcbond_other	1.226	2.172	15443
X-RAY DIFFRACTION	r_mcangle_it	1.999	3.253	19284
X-RAY DIFFRACTION	r_mcangle_other	1.999	3.253	19285
X-RAY DIFFRACTION	r_scbond_it	1.555	2.384	15784
X-RAY DIFFRACTION	r_scbond_other	1.555	2.384	15785
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.536	3.513	23405
X-RAY DIFFRACTION	r_long_range_B_refined	6.399	18.672	36958
X-RAY DIFFRACTION	r_long_range_B_other	6.346	18.276	36286
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.267→2.326 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.317	682	-
R_work	0.298	12407	-
obs	-	-	92.18 %

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	0.6206	0.1051	-0.3738	1.1305	-0.2313	0.7492	0.0235	-0.0343	-0.0331	-0.0385	0.0335	-0.0853	-0.082	0.1182	-0.057	0.1614	-0.0213	0.0275	0.1996	-0.0281	0.2041	90.0071	20.0198	46.5037
2	0.6849	0.2245	-0.2676	1.0391	0.3148	0.9009	0.0642	0.1007	0.006	0.0106	0.0088	0.0749	-0.1562	-0.1192	-0.073	0.1721	0.0372	0.0228	0.1868	0.0256	0.2118	57.3365	20.2735	53.3525
3	0.6188	-0.0838	-0.1796	0.8128	-0.0685	0.9459	-0.0392	0.0855	-0.0365	-0.0759	0.0371	-0.0756	0.1948	0.0217	0.0021	0.2319	0.0158	0.0338	0.1515	-0.0353	0.192	80.609	-20.8285	33.8477
4	0.5917	0.1427	-0.098	0.8018	0.0852	1.3543	-0.0068	-0.0018	-0.0285	0.081	0.0282	0.0065	0.2243	-0.0721	-0.0215	0.232	-0.0169	0.0188	0.1254	0.0049	0.1999	65.1399	-21.0557	63.3572
5	0.7685	0.0407	0.2823	0.9919	0.6066	2.2158	-0.0068	0.0305	0.1774	-0.014	-0.078	-0.0205	-0.4212	0.1607	0.0848	0.1597	0.0059	0.0396	0.2238	-0.0387	0.1813	110.3497	27.0774	12.6361
6	1.0009	-0.147	0.0304	0.8063	-0.2705	1.1573	0.0399	0.0642	0.0777	-0.0239	-0.0048	0.0009	-0.123	-0.0718	-0.035	0.1836	0.0082	0.0257	0.0993	0.0173	0.2402	118.6892	28.9628	86.4155
7	0.7995	0.2043	-0.055	0.5988	0.0233	2.2287	0.0232	0.0622	-0.0121	0.0386	0.0552	0.0136	0.2491	-0.2025	-0.0784	0.1271	0.0584	0.0709	0.2612	0.0164	0.1414	94.1652	-6.0669	-10.0516
8	0.8152	0.2649	-0.0033	0.5669	0.1363	1.0893	-0.0439	0.0407	-0.019	0.0611	0.0398	0.0146	0.0608	-0.0196	0.0041	0.1853	0.018	0.0695	0.1103	-0.0133	0.241	76.4167	61.0351	85.4165
9	0.8436	0.3035	-0.2882	0.9219	0.2892	1.1408	-0.0497	0.1731	-0.0157	-0.104	0.1282	-0.0767	-0.1406	0.1054	-0.0785	0.1822	-0.0566	0.084	0.189	-0.0149	0.1961	96.473	72.7733	61.3645
10	0.6686	-0.2472	-0.0102	0.9399	-0.1227	2.0646	-0.0102	-0.2388	0.0344	0.115	0.0775	0.059	-0.117	-0.3402	-0.0673	0.1244	-0.0379	0.1094	0.3668	-0.0157	0.1096	114.558	5.458	-33.854
11	1.0652	-0.4556	0.1637	1.4124	-0.2408	0.9498	-0.0147	-0.11	-0.1465	-0.0393	0.0812	0.3751	-0.075	-0.3344	-0.0664	0.0417	0.0222	0.0399	0.2006	0.0539	0.3577	89.7688	16.5461	97.4669
12	1.0504	0.21	0.3028	1.3315	0.2637	0.7441	0.0749	0.3249	0.122	-0.0701	-0.1804	-0.2957	-0.0149	0.5322	0.1055	0.0354	-0.0228	0.0849	0.5983	0.0778	0.2667	139.33	14.574	1.633

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	9 - 330
2	X-RAY DIFFRACTION	2	B	9 - 330
3	X-RAY DIFFRACTION	3	C	9 - 330
4	X-RAY DIFFRACTION	4	D	9 - 330
5	X-RAY DIFFRACTION	5	E	9 - 330
6	X-RAY DIFFRACTION	6	F	9 - 330
7	X-RAY DIFFRACTION	7	G	9 - 330
8	X-RAY DIFFRACTION	8	H	9 - 330
9	X-RAY DIFFRACTION	9	I	9 - 330
10	X-RAY DIFFRACTION	10	J	9 - 330
11	X-RAY DIFFRACTION	11	K	9 - 330
12	X-RAY DIFFRACTION	12	L	9 - 330

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