PDB-9ou5: Crystal Structure of Salmonella FraB Deglycase, Crystal Form 3

ID or keywords:

Entry

Database: PDB / ID: 9ou5

Title

Crystal Structure of Salmonella FraB Deglycase, Crystal Form 3

Components

SIS domain protein

Keywords

ANTIBIOTIC / FraB deglycase / Salmonella / Amadori compounds / Fructose-asparagine

Function / homology

Function and homology information

glutamine-fructose-6-phosphate transaminase (isomerizing) activity / UDP-N-acetylglucosamine metabolic process / carbohydrate derivative binding / protein N-linked glycosylation / fructose 6-phosphate metabolic process
Similarity search - Function

Biological species

Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.669 Å

Authors

Bell, C.E. / Zakharova, K.

Funding support

United States, 1items

Citation

Journal: Protein Sci. / Year: 2025
Title: Crystal structures of Salmonella enterica FraB deglycase reveal a conformational heterodimer with remarkable structural plasticity at the active site.
Authors: Zakharova, K. / Law, J.D. / Gao, Y. / Kovvali, S. / Wysocki, V.H. / Gopalan, V. / Bell, C.E.

History

Deposition	May 28, 2025	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 6, 2025	Provider: repository / Type: Initial release
Revision 1.1	Sep 3, 2025	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9ou5.cif.gz	147.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9ou5.ent.gz	109.3 KB	Display	PDB format
PDBx/mmJSON format	9ou5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9ou5_validation.pdf.gz	438.5 KB	Display	wwPDB validaton report
Full document	9ou5_full_validation.pdf.gz	444.5 KB	Display
Data in XML	9ou5_validation.xml.gz	32.1 KB	Display
Data in CIF	9ou5_validation.cif.gz	44.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ou/9ou5 ftp://data.pdbj.org/pub/pdb/validation_reports/ou/9ou5	HTTPS FTP

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Related structure data

Related structure data	9otjC 9otlC 9otrC 9otuC 9ou6C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SIS domain protein

B: SIS domain protein

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

1

Idetical with deposited unit
defined by author&software
Evidence: mass spectrometry

Unit cell

Length a, b, c (Å)	58.574, 110.614, 115.530
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	SIS domain protein / FraB Deglycase Mass: 38772.652 Da / Num. of mol.: 2 / Mutation: K275A,E276A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria) Gene: A628_00340 / Production host: Escherichia coli (E. coli) / References: UniProt: V7IWJ0
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.41 Å³/Da / Density % sol: 49.03 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10-14% v/v PEG300, 0.1 M MES, pH 6.0-6.5 / PH range: 6.0-6.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 1.669→79.9 Å / Num. obs: 67143 / % possible obs: 76.4 % / Redundancy: 12.9 % / R_merge(I) obs: 0.076 / R_pim(I) all: 0.022 / Net I/σ(I): 16.7
Reflection shell	Resolution: 1.67→1.828 Å / R_merge(I) obs: 1.419 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3357 / R_pim(I) all: 0.442

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS	Feb 5, 2021 (BUILT 20210205)	data reduction
Aimless	0.7.4	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.669→79.897 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.955 / SU B: 2.441 / SU ML: 0.076 / Cross valid method: FREE R-VALUE / ESU R: 0.111 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2021	3329	4.958 %
R_work	0.1708	63814	-
all	0.172	-	-
obs	-	67143	76.39 %

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: 31.89 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.126 Å²	0 Å²	-0 Å²
2-	-	-0.099 Å²	-0 Å²
3-	-	-	-0.027 Å²

Refinement step

Cycle: LAST / Resolution: 1.669→79.897 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4831	0	0	414	5245

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.012	4945
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4525
X-RAY DIFFRACTION	r_angle_refined_deg	1.712	1.802	6711
X-RAY DIFFRACTION	r_angle_other_deg	0.6	1.738	10388
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.527	5	620
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	8.232	5	18
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.821	10	764
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.508	10	233
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	731
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5878
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1178
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1037
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.189	0.2	4193
X-RAY DIFFRACTION	r_nbtor_refined	0.186	0.2	2535
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	2673
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.169	0.2	337
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.128	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.1	0.2	4
X-RAY DIFFRACTION	r_nbd_other	0.156	0.2	25
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.143	0.2	8
X-RAY DIFFRACTION	r_mcbond_it	2.947	3.173	2492
X-RAY DIFFRACTION	r_mcbond_other	2.945	3.173	2492
X-RAY DIFFRACTION	r_mcangle_it	3.885	5.685	3108
X-RAY DIFFRACTION	r_mcangle_other	3.884	5.686	3109
X-RAY DIFFRACTION	r_scbond_it	4.256	3.697	2453
X-RAY DIFFRACTION	r_scbond_other	4.252	3.697	2453
X-RAY DIFFRACTION	r_scangle_it	6.448	6.56	3603
X-RAY DIFFRACTION	r_scangle_other	6.447	6.561	3604
X-RAY DIFFRACTION	r_lrange_it	7.827	32.236	5775
X-RAY DIFFRACTION	r_lrange_other	7.744	31.79	5693

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	R_factor all	Num. reflection all	Fsc free	Fsc work	% reflection obs (%)	WR_factor R_work
1.669-1.713	0.411	8	0.353	159	0.356	6399	0.875	0.899	2.6098	0.342
1.713-1.76	0.334	43	0.31	701	0.311	6259	0.926	0.927	11.8869	0.303
1.76-1.811	0.314	89	0.277	1600	0.279	6095	0.926	0.946	27.7112	0.273
1.811-1.866	0.255	132	0.25	2639	0.251	5911	0.949	0.955	46.8787	0.233
1.866-1.927	0.275	238	0.25	4260	0.251	5753	0.943	0.955	78.1853	0.23
1.927-1.995	0.233	255	0.229	5204	0.229	5548	0.964	0.962	98.3958	0.199
1.995-2.07	0.223	269	0.212	5090	0.213	5365	0.966	0.969	99.8882	0.179
2.07-2.155	0.213	273	0.187	4925	0.188	5205	0.971	0.977	99.8655	0.157
2.155-2.25	0.216	245	0.172	4711	0.174	4962	0.969	0.981	99.8791	0.142
2.25-2.36	0.209	235	0.163	4533	0.165	4774	0.973	0.983	99.8743	0.134
2.36-2.488	0.179	219	0.152	4271	0.153	4501	0.98	0.986	99.7556	0.129
2.488-2.639	0.185	224	0.15	4085	0.152	4315	0.979	0.987	99.8609	0.13
2.639-2.82	0.181	217	0.157	3826	0.158	4047	0.981	0.986	99.9012	0.14
2.82-3.046	0.195	176	0.158	3620	0.16	3800	0.976	0.985	99.8947	0.151
3.046-3.336	0.207	160	0.172	3321	0.174	3486	0.97	0.981	99.8566	0.172
3.336-3.729	0.22	159	0.176	3005	0.178	3170	0.971	0.982	99.8107	0.184
3.729-4.305	0.211	129	0.15	2700	0.152	2832	0.976	0.986	99.8941	0.165
4.305-5.268	0.167	112	0.146	2293	0.147	2411	0.978	0.987	99.7511	0.173
5.268-7.435	0.246	91	0.184	1817	0.187	1910	0.968	0.981	99.8953	0.213
7.435-79.897	0.138	55	0.182	1054	0.18	1124	0.985	0.973	98.6655	0.243

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