PDB-9qgh: BV333 aminotransferase from Streptomyces sp. mutant F61C

ID or keywords:

Entry

Database: PDB / ID: 9qgh

Title

BV333 aminotransferase from Streptomyces sp. mutant F61C

Components

Aspartate aminotransferase family protein

Keywords

TRANSFERASE

Function / homology

Function and homology information

biosynthetic process / transaminase activity / pyridoxal phosphate binding
Similarity search - Function

Biological species

Streptomyces sp. BV333 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.31 Å

Authors

De Rose, S.A. / Isupov, M.N. / Patti, S.

Funding support

1items

Citation

Journal: Appl.Microbiol.Biotechnol. / Year: 2025
Title: Functional and structural insights into a thermostable (S)-selective amine transaminase and its improved substrate scope by protein engineering.
Authors: Patti, S. / De Rose, S.A. / Isupov, M.N. / Magrini Alunno, I. / Riva, S. / Ferrandi, E.E. / Littlechild, J.A. / Monti, D.

History

Deposition	Mar 13, 2025	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Mar 18, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9qgh.cif.gz	207 KB	Display	PDBx/mmCIF format
PDB format	pdb9qgh.ent.gz	156.9 KB	Display	PDB format
PDBx/mmJSON format	9qgh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/qg/9qgh ftp://data.pdbj.org/pub/pdb/validation_reports/qg/9qgh	HTTPS FTP

-
Related structure data

Related structure data	9gh9C 9gnfC 9qc2C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Aspartate aminotransferase family protein

B: Aspartate aminotransferase family protein

99.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Aspartate aminotransferase family protein

B: Aspartate aminotransferase family protein

A: Aspartate aminotransferase family protein

B: Aspartate aminotransferase family protein

defined by software
Evidence: gel filtration
200 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.747, 176.464, 111.259
Angle α, β, γ (deg.)	90, 90, 90
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	A-664- HOH
2	1	B-641- HOH
3	1	B-699- HOH
4	1	B-796- HOH
5	1	B-803- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 9 - 459 / Label seq-ID: 1 - 451

Dom-ID	Auth asym-ID	Label asym-ID
1	A	A
2	B	B

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

#1: Protein	Aspartate aminotransferase family protein Mass: 49903.004 Da / Num. of mol.: 2 / Mutation: F61C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces sp. BV333 (bacteria) / Gene: OIM89_06295 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0AA46ZEV9
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
Has protein modification	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.45 Å³/Da / Density % sol: 49.85 %
Crystal grow	Temperature: 292.15 K / Method: microbatch / Details: Morpheus Fusion Screen A7 / Temp details: Memmert incubator

-
Data collection

Diffraction	Mean temperature: 113.15 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.852 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 12, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.852 Å / Relative weight: 1
Reflection	Resolution: 1.31→88.23 Å / Num. obs: 221445 / % possible obs: 94.75 % / Redundancy: 6 % / B_iso Wilson estimate: 19.77 Å² / CC_1/2: 1 / R_rim(I) all: 0.069 / Net I/σ(I): 8.9
Reflection shell	Resolution: 1.31→1.33 Å / Redundancy: 2.9 % / Num. unique obs: 7504 / CC_1/2: 0.3 / R_rim(I) all: 2.047 / % possible all: 64.8

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.100)	refinement
xia2	3.9	data reduction
XSCALE		data scaling
MoRDa		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.31→88.23 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.97 / SU B: 1.875 / SU ML: 0.065 / Cross valid method: FREE R-VALUE / ESU R: 0.051 / ESU R Free: 0.053 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2102	2041	0.922 %
R_work	0.1879	219340	-
all	0.188	-	-
obs	-	221381	94.749 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 27.831 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.304 Å²	0 Å²	-0 Å²
2-	-	-0.529 Å²	-0 Å²
3-	-	-	0.832 Å²

Refinement step

Cycle: LAST / Resolution: 1.31→88.23 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7044	0	0	601	7645

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.019	0.012	7236
X-RAY DIFFRACTION	r_angle_refined_deg	2.411	1.814	9846
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.45	5	900
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	11.447	5	44
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.091	10	1098
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	16.699	10	336
X-RAY DIFFRACTION	r_chiral_restr	0.206	0.2	1060
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.02	5666
X-RAY DIFFRACTION	r_nbd_refined	0.193	0.2	3401
X-RAY DIFFRACTION	r_nbtor_refined	0.299	0.2	4945
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	608
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.137	0.2	461
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.108	0.2	73
X-RAY DIFFRACTION	r_mcbond_it	2.759	2.416	3606
X-RAY DIFFRACTION	r_mcangle_it	3.607	4.348	4504
X-RAY DIFFRACTION	r_scbond_it	5.382	2.826	3630
X-RAY DIFFRACTION	r_scangle_it	7.671	5.007	5342
X-RAY DIFFRACTION	r_lrange_it	8.059	30.716	11457
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.042	0.05	15149

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.04229	0.05008
1	2	B	X-RAY DIFFRACTION	Local ncs	0.04229	0.05008

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.31-1.344	0.388	125	0.402	11353	X-RAY DIFFRACTION	66.8569
1.344-1.381	0.378	117	0.389	12930	X-RAY DIFFRACTION	78.0743
1.381-1.421	0.395	148	0.373	14353	X-RAY DIFFRACTION	88.9686
1.421-1.465	0.388	140	0.371	14986	X-RAY DIFFRACTION	95.5467
1.465-1.513	0.352	133	0.35	14858	X-RAY DIFFRACTION	97.9932
1.513-1.566	0.34	180	0.329	14586	X-RAY DIFFRACTION	99.5953
1.566-1.625	0.327	152	0.294	14157	X-RAY DIFFRACTION	100
1.625-1.691	0.286	121	0.251	13710	X-RAY DIFFRACTION	100
1.691-1.766	0.23	108	0.218	13112	X-RAY DIFFRACTION	100
1.766-1.852	0.244	116	0.194	12558	X-RAY DIFFRACTION	100
1.852-1.953	0.201	83	0.165	11998	X-RAY DIFFRACTION	100
1.953-2.071	0.204	89	0.173	11327	X-RAY DIFFRACTION	100
2.071-2.214	0.198	67	0.173	10670	X-RAY DIFFRACTION	100
2.214-2.391	0.211	93	0.165	9927	X-RAY DIFFRACTION	100
2.391-2.619	0.187	84	0.164	9162	X-RAY DIFFRACTION	99.9892
2.619-2.928	0.182	92	0.157	8300	X-RAY DIFFRACTION	99.9881
2.928-3.38	0.168	60	0.155	7370	X-RAY DIFFRACTION	100
3.38-4.138	0.144	54	0.143	6265	X-RAY DIFFRACTION	100
4.138-5.846	0.166	41	0.153	4900	X-RAY DIFFRACTION	100
5.846-88.23	0.207	38	0.204	2807	X-RAY DIFFRACTION	100

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi