PDB-9otu: Crystal Structure of Salmonella FraB Deglycase, E214A Mutant, Cry...

ID or keywords:

Entry

Database: PDB / ID: 9otu

Title

Crystal Structure of Salmonella FraB Deglycase, E214A Mutant, Crystal Form 5

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: 1.873 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 27, 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	9otu.cif.gz	133.5 KB	Display	PDBx/mmCIF format
PDB format	pdb9otu.ent.gz	99.7 KB	Display	PDB format
PDBx/mmJSON format	9otu.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	9otu_validation.pdf.gz	445.1 KB	Display	wwPDB validaton report
Full document	9otu_full_validation.pdf.gz	481.4 KB	Display
Data in XML	9otu_validation.xml.gz	29.7 KB	Display
Data in CIF	9otu_validation.cif.gz	37.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ot/9otu ftp://data.pdbj.org/pub/pdb/validation_reports/ot/9otu	HTTPS FTP

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Related structure data

Related structure data	9otjC 9otlC 9otrC 9ou5C 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

77.4 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)	114.417, 114.417, 154.469
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21

#1: Protein	SIS domain protein / FraB Deglycase Mass: 38714.621 Da / Num. of mol.: 2 / Mutation: K275A,E276A,E214A 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.: 60 / 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: 3.77 Å³/Da / Density % sol: 67.37 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 18% w/v PEG6000, 0.2 M magnesium chloride, 0.1 M MES, pH 6.0

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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: Jul 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97931 Å / Relative weight: 1
Reflection	Resolution: 1.873→99.088 Å / Num. obs: 35409 / % possible obs: 36.7 % / Redundancy: 9.6 % / R_merge(I) obs: 0.078 / R_pim(I) all: 0.026 / Net I/σ(I): 15.8
Reflection shell	Resolution: 1.873→2.152 Å / R_merge(I) obs: 0.886 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1769 / R_pim(I) all: 0.354

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS	Feb 5, 2021 (BUILT 20210205)	data reduction
Aimless	0.7.7	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.873→99.088 Å / Cor.coef. F_o:F_c: 0.894 / Cor.coef. F_o:F_c free: 0.826 / SU B: 6.872 / SU ML: 0.192 / Cross valid method: FREE R-VALUE / ESU R: 0.402 / ESU R Free: 0.331
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3333	1718	4.852 %
R_work	0.2683	33691	-
all	0.272	-	-
obs	-	35409	36.72 %

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: 40.453 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.022 Å²	-0.011 Å²	-0 Å²
2-	-	-0.022 Å²	0 Å²
3-	-	-	0.071 Å²

Refinement step

Cycle: LAST / Resolution: 1.873→99.088 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4649	0	0	60	4709

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.012	4757
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4341
X-RAY DIFFRACTION	r_angle_refined_deg	1.761	1.795	6466
X-RAY DIFFRACTION	r_angle_other_deg	0.596	1.732	9947
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	9.084	5	603
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	5.464	5	17
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	18.273	10	715
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.564	10	219
X-RAY DIFFRACTION	r_chiral_restr	0.08	0.2	716
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	5665
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1133
X-RAY DIFFRACTION	r_nbd_refined	0.242	0.2	1378
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.213	0.2	4870
X-RAY DIFFRACTION	r_nbtor_refined	0.194	0.2	2368
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2658
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.208	0.2	200
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.029	0.2	9
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.211	0.2	7
X-RAY DIFFRACTION	r_nbd_other	0.169	0.2	39
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.243	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	3.654	4.12	2424
X-RAY DIFFRACTION	r_mcbond_other	3.654	4.12	2424
X-RAY DIFFRACTION	r_mcangle_it	5.697	7.392	3023
X-RAY DIFFRACTION	r_mcangle_other	5.696	7.393	3024
X-RAY DIFFRACTION	r_scbond_it	3.417	4.334	2333
X-RAY DIFFRACTION	r_scbond_other	3.416	4.335	2334
X-RAY DIFFRACTION	r_scangle_it	5.525	7.875	3443
X-RAY DIFFRACTION	r_scangle_other	5.525	7.876	3444
X-RAY DIFFRACTION	r_lrange_it	8.368	39.286	5728
X-RAY DIFFRACTION	r_lrange_other	8.368	39.288	5729

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
1.873-1.922	0.289	2	0.457	79	0.452	7044	0.995	0.776	1.1499	0.442
1.922-1.975	0.372	12	0.453	216	0.448	6896	0.882	0.816	3.3063	0.434
1.975-2.032	0.418	15	0.38	383	0.381	6666	0.894	0.89	5.9706	0.357
2.032-2.094	0.607	35	0.398	480	0.412	6513	0.788	0.886	7.9073	0.387
2.094-2.163	0.373	34	0.358	612	0.359	6336	0.885	0.907	10.1957	0.337
2.163-2.239	0.422	40	0.364	679	0.367	6102	0.854	0.907	11.783	0.347
2.239-2.323	0.48	39	0.36	847	0.365	5881	0.851	0.903	15.0655	0.322
2.323-2.418	0.383	41	0.329	985	0.332	5701	0.915	0.916	17.9968	0.299
2.418-2.525	0.45	60	0.292	1203	0.298	5426	0.842	0.94	23.2768	0.258
2.525-2.649	0.375	63	0.3	1374	0.304	5242	0.919	0.931	27.4132	0.271
2.649-2.792	0.353	71	0.294	1784	0.296	4999	0.918	0.937	37.1074	0.262
2.792-2.961	0.351	122	0.298	2221	0.301	4697	0.921	0.937	49.8829	0.271
2.961-3.165	0.404	154	0.319	3474	0.323	4447	0.886	0.925	81.5831	0.29
3.165-3.419	0.41	191	0.314	3916	0.318	4123	0.872	0.93	99.6119	0.305
3.419-3.744	0.36	202	0.288	3637	0.292	3840	0.906	0.944	99.974	0.27
3.744-4.186	0.362	158	0.25	3318	0.255	3484	0.918	0.958	99.7704	0.24
4.186-4.832	0.255	156	0.226	2909	0.227	3083	0.956	0.967	99.4162	0.232
4.832-5.914	0.278	147	0.241	2478	0.243	2625	0.951	0.962	100	0.254
5.914-8.349	0.317	107	0.238	1977	0.242	2087	0.938	0.961	99.8563	0.266
8.349-99.088	0.263	69	0.225	1118	0.227	1216	0.945	0.965	97.6151	0.297

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