PDB-6eod: Structure of Reductive Aminase from Aspergillus terreus in comple...

ID or keywords:

Entry

Database: PDB / ID: 6eod

Title

Structure of Reductive Aminase from Aspergillus terreus in complex with NADPH

Components

Reductive Aminase

Keywords

OXIDOREDUCTASE / Amine / Imine / NADPH

Function / homology

Function and homology information

transcription elongation-coupled chromatin remodeling / nucleosome binding / NADP binding / oxidoreductase activity / chromatin / DNA binding
Similarity search - Function

Biological species

Aspergillus terreus (mold)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Sharma, M. / Mangas-Sanchez, J. / Turner, N.J. / Grogan, G.

Funding support

United Kingdom, 1items

Citation

Journal: Acs Catalysis / Year: 2018
Title: A Mechanism for Reductive Amination Catalyzed by Fungal Reductive Aminases
Authors: Sharma, M. / Mangas-Sanchez, J. / Turner, N.J. / Grogan, G.

History

Deposition	Oct 9, 2017	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 31, 2018	Provider: repository / Type: Initial release
Revision 1.1	Nov 13, 2019	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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2	Jan 17, 2024	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6eod.cif.gz	417.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6eod.ent.gz	338.5 KB	Display	PDB format
PDBx/mmJSON format	6eod.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/eo/6eod ftp://data.pdbj.org/pub/pdb/validation_reports/eo/6eod	HTTPS FTP

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Related structure data

Related structure data	6eohC 6eoiC 5g6rS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3o8q-d 5a9r-1 2pv7-d 4o8k-d 1zp2-2 3pgj-2 3mtv-1 4gbj-2 3cky-2 1kap-d 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

6eohC

6eoiC

5g6rS

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	#127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: Reductive Aminase

B: Reductive Aminase

C: Reductive Aminase

D: Reductive Aminase

F: Reductive Aminase

G: Reductive Aminase

E: Reductive Aminase

H: Reductive Aminase

hetero molecules

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

1

A: Reductive Aminase

H: Reductive Aminase

hetero molecules

defined by author&software
Evidence: gel filtration
62.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Reductive Aminase

G: Reductive Aminase

hetero molecules

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

3

C: Reductive Aminase

D: Reductive Aminase

hetero molecules

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

4

F: Reductive Aminase

E: Reductive Aminase

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

Unit cell

Length a, b, c (Å)	75.977, 85.552, 355.423
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Beg auth comp-ID: THR / Beg label comp-ID: THR / Refine code: _

Dom-ID	Ens-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	ARG	ARG	A	A	6 - 294	6 - 294
2	1	ARG	ARG	B	B	6 - 294	6 - 294
1	2	ARG	ARG	A	A	7 - 294	7 - 294
2	2	ARG	ARG	C	C	7 - 294	7 - 294
1	3	ARG	ARG	A	A	6 - 294	6 - 294
2	3	ARG	ARG	D	D	6 - 294	6 - 294
1	4	PHE	PHE	A	A	7 - 293	7 - 293
2	4	PHE	PHE	F	E	7 - 293	7 - 293
1	5	ARG	ARG	A	A	11 - 294	11 - 294
2	5	ARG	ARG	G	F	11 - 294	11 - 294
1	6	ARG	ARG	A	A	6 - 294	6 - 294
2	6	ARG	ARG	E	G	6 - 294	6 - 294
1	7	ARG	ARG	A	A	6 - 294	6 - 294
2	7	ARG	ARG	H	H	6 - 294	6 - 294
1	8	ARG	ARG	B	B	7 - 294	7 - 294
2	8	ARG	ARG	C	C	7 - 294	7 - 294
1	9	ARG	ARG	B	B	6 - 294	6 - 294
2	9	ARG	ARG	D	D	6 - 294	6 - 294
1	10	PHE	PHE	B	B	7 - 293	7 - 293
2	10	PHE	PHE	F	E	7 - 293	7 - 293
1	11	ARG	ARG	B	B	11 - 294	11 - 294
2	11	ARG	ARG	G	F	11 - 294	11 - 294
1	12	ARG	ARG	B	B	6 - 294	6 - 294
2	12	ARG	ARG	E	G	6 - 294	6 - 294
1	13	ARG	ARG	B	B	6 - 294	6 - 294
2	13	ARG	ARG	H	H	6 - 294	6 - 294
1	14	ARG	ARG	C	C	7 - 294	7 - 294
2	14	ARG	ARG	D	D	7 - 294	7 - 294
1	15	PHE	PHE	C	C	7 - 293	7 - 293
2	15	PHE	PHE	F	E	7 - 293	7 - 293
1	16	ARG	ARG	C	C	11 - 294	11 - 294
2	16	ARG	ARG	G	F	11 - 294	11 - 294
1	17	ARG	ARG	C	C	8 - 294	8 - 294
2	17	ARG	ARG	E	G	8 - 294	8 - 294
1	18	ARG	ARG	C	C	7 - 294	7 - 294
2	18	ARG	ARG	H	H	7 - 294	7 - 294
1	19	PHE	PHE	D	D	7 - 293	7 - 293
2	19	PHE	PHE	F	E	7 - 293	7 - 293
1	20	ARG	ARG	D	D	11 - 294	11 - 294
2	20	ARG	ARG	G	F	11 - 294	11 - 294
1	21	ASN	ASN	D	D	6 - 295	6 - 295
2	21	ASN	ASN	E	G	6 - 295	6 - 295
1	22	ASN	ASN	D	D	6 - 295	6 - 295
2	22	ASN	ASN	H	H	6 - 295	6 - 295
1	23	PHE	PHE	F	E	11 - 293	11 - 293
2	23	PHE	PHE	G	F	11 - 293	11 - 293
1	24	PHE	PHE	F	E	8 - 293	8 - 293
2	24	PHE	PHE	E	G	8 - 293	8 - 293
1	25	PHE	PHE	F	E	7 - 293	7 - 293
2	25	PHE	PHE	H	H	7 - 293	7 - 293
1	26	ARG	ARG	G	F	11 - 294	11 - 294
2	26	ARG	ARG	E	G	11 - 294	11 - 294
1	27	ARG	ARG	G	F	11 - 294	11 - 294
2	27	ARG	ARG	H	H	11 - 294	11 - 294
1	28	ASN	ASN	E	G	6 - 295	6 - 295
2	28	ASN	ASN	H	H	6 - 295	6 - 295

NCS ensembles :

#1: Protein	Reductive Aminase Mass: 30756.084 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aspergillus terreus (mold) / Gene: ATEG_08501 / Plasmid: pET-YSBLIC-3C / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q0CCT3
#2: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 823 / 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: 2.4 Å³/Da / Density % sol: 49 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 31% (w/v) PEG 3350; 0.2 M MgCl2, 0.1 M Tris HCl pH 7.5

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Data collection

Diffraction	Mean temperature: 120 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 16, 2015
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2.2→177.71 Å / Num. obs: 118787 / % possible obs: 100 % / Redundancy: 8.1 % / CC_1/2: 1 / R_merge(I) obs: 0.1 / R_pim(I) all: 0.05 / Net I/σ(I): 13.2
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 8.3 % / R_merge(I) obs: 0.73 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5820 / CC_1/2: 0.83 / R_pim(I) all: 0.4 / % possible all: 100

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
xia2		data reduction
XDS		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5G6R

5g6r

Resolution: 2.2→177.71 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.929 / SU B: 6.117 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.203 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23581	5951	5 %	RANDOM
R_work	0.19848	-	-	-
obs	0.20035	112724	99.96 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 41.387 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.89 Å²	-0 Å²	-0 Å²
2-	-	0.8 Å²	-0 Å²
3-	-	-	-1.69 Å²

Refinement step

Cycle: 1 / Resolution: 2.2→177.71 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15643	0	144	823	16610

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.015	0.019	16066
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	14931
X-RAY DIFFRACTION	r_angle_refined_deg	1.748	1.983	21906
X-RAY DIFFRACTION	r_angle_other_deg	1.067	3	34271
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.222	5	2194
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.597	23.385	520
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.144	15	2276
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	22.559	15	79
X-RAY DIFFRACTION	r_chiral_restr	0.12	0.2	2643
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	18250
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	3192
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	3.845	4.212	8842
X-RAY DIFFRACTION	r_mcbond_other	3.844	4.212	8841
X-RAY DIFFRACTION	r_mcangle_it	5.448	6.293	11005
X-RAY DIFFRACTION	r_mcangle_other	5.448	6.293	11006
X-RAY DIFFRACTION	r_scbond_it	4.451	4.404	7224
X-RAY DIFFRACTION	r_scbond_other	4.451	4.403	7225
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	6.428	6.512	10899
X-RAY DIFFRACTION	r_long_range_B_refined	8.254	50.43	17672
X-RAY DIFFRACTION	r_long_range_B_other	8.243	50.359	17533
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	16522	0.07
1	2	B	16522	0.07
2	1	A	16136	0.07
2	2	C	16136	0.07
3	1	A	16054	0.07
3	2	D	16054	0.07
4	1	A	13762	0.08
4	2	F	13762	0.08
5	1	A	14072	0.09
5	2	G	14072	0.09
6	1	A	16068	0.07
6	2	E	16068	0.07
7	1	A	15994	0.09
7	2	H	15994	0.09
8	1	B	16188	0.07
8	2	C	16188	0.07
9	1	B	15968	0.08
9	2	D	15968	0.08
10	1	B	13694	0.08
10	2	F	13694	0.08
11	1	B	14032	0.08
11	2	G	14032	0.08
12	1	B	16040	0.07
12	2	E	16040	0.07
13	1	B	16070	0.09
13	2	H	16070	0.09
14	1	C	15914	0.08
14	2	D	15914	0.08
15	1	C	13542	0.08
15	2	F	13542	0.08
16	1	C	14022	0.07
16	2	G	14022	0.07
17	1	C	15722	0.07
17	2	E	15722	0.07
18	1	C	15704	0.08
18	2	H	15704	0.08
19	1	D	13648	0.08
19	2	F	13648	0.08
20	1	D	14214	0.08
20	2	G	14214	0.08
21	1	D	16072	0.06
21	2	E	16072	0.06
22	1	D	16000	0.07
22	2	H	16000	0.07
23	1	F	12798	0.09
23	2	G	12798	0.09
24	1	F	13670	0.07
24	2	E	13670	0.07
25	1	F	13744	0.08
25	2	H	13744	0.08
26	1	G	14120	0.08
26	2	E	14120	0.08
27	1	G	14272	0.08
27	2	H	14272	0.08
28	1	E	16138	0.07
28	2	H	16138	0.07

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.302	462	-
R_work	0.259	8194	-
obs	-	-	100 %

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