PDB-9otr: Crystal Structure of Salmonella FraB Deglycase, Crystal Form 4 wi...

ID or keywords:

Entry

Database: PDB / ID: 9otr

Title

Crystal Structure of Salmonella FraB Deglycase, Crystal Form 4 with deletion of C-terminal residues 313-325.

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: 1.839 Å

Authors

Bell, C.E. / Zakharova, K.

Funding support

United States, 1items

Citation

Journal: To Be Published
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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9otr.cif.gz	141.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9otr.ent.gz	105.1 KB	Display	PDB format
PDBx/mmJSON format	9otr.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9otr_validation.pdf.gz	434 KB	Display	wwPDB validaton report
Full document	9otr_full_validation.pdf.gz	441.7 KB	Display
Data in XML	9otr_validation.xml.gz	30.6 KB	Display
Data in CIF	9otr_validation.cif.gz	41.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ot/9otr ftp://data.pdbj.org/pub/pdb/validation_reports/ot/9otr	HTTPS FTP

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Related structure data

Related structure data	9otjC 9otlC 9otuC 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

74.1 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)	55.482, 108.363, 119.151
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 / C-terminal truncation Mass: 37044.613 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.: 310 / 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: 2.42 Å³/Da / Density % sol: 49.12 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 20% w/v PEG3350, 0.2 M sodium sulfate, 0.1 M Bis-Tris propane, pH 8.0-8.5 PH range: 8.0-8.5

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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: 0.97933 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 10, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97933 Å / Relative weight: 1
Reflection	Resolution: 1.839→49.434 Å / Num. obs: 45084 / % possible obs: 71.2 % / Redundancy: 5.9 % / R_merge(I) obs: 0.065 / R_pim(I) all: 0.041 / Net I/σ(I): 16.7
Reflection shell	Resolution: 1.839→1.987 Å / R_merge(I) obs: 0.919 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2254 / R_sym value: 0.419

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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: 1.839→49.434 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.952 / SU B: 3.596 / SU ML: 0.1 / Cross valid method: FREE R-VALUE / ESU R: 0.169 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2042	2238	4.964 %
R_work	0.1724	42846	-
all	0.174	-	-
obs	-	45084	71.223 %

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: 35.602 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.141 Å²	0 Å²	-0 Å²
2-	-	-0.184 Å²	0 Å²
3-	-	-	0.325 Å²

Refinement step

Cycle: LAST / Resolution: 1.839→49.434 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4697	0	0	310	5007

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	4807
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4413
X-RAY DIFFRACTION	r_angle_refined_deg	1.684	1.8	6523
X-RAY DIFFRACTION	r_angle_other_deg	0.574	1.738	10125
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.197	5	605
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.548	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.44	10	744
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	13.905	10	225
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	713
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5721
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1151
X-RAY DIFFRACTION	r_nbd_refined	0.217	0.2	1094
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.194	0.2	4320
X-RAY DIFFRACTION	r_nbtor_refined	0.187	0.2	2427
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.084	0.2	2614
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.175	0.2	283
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.171	0.2	13
X-RAY DIFFRACTION	r_nbd_other	0.201	0.2	59
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.161	0.2	13
X-RAY DIFFRACTION	r_mcbond_it	3.129	3.528	2429
X-RAY DIFFRACTION	r_mcbond_other	3.126	3.528	2429
X-RAY DIFFRACTION	r_mcangle_it	4.424	6.328	3031
X-RAY DIFFRACTION	r_mcangle_other	4.424	6.329	3032
X-RAY DIFFRACTION	r_scbond_it	4.296	4.098	2378
X-RAY DIFFRACTION	r_scbond_other	4.295	4.1	2379
X-RAY DIFFRACTION	r_scangle_it	6.587	7.303	3492
X-RAY DIFFRACTION	r_scangle_other	6.586	7.304	3493
X-RAY DIFFRACTION	r_lrange_it	8.473	38.029	5637
X-RAY DIFFRACTION	r_lrange_other	8.449	37.945	5568

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
1.839-1.886	0.231	6	0.306	94	0.301	4612	0.959	0.925	2.1683	0.29
1.886-1.938	0.309	30	0.335	663	0.334	4524	0.928	0.929	15.3183	0.333
1.938-1.994	0.278	70	0.262	1673	0.263	4374	0.937	0.954	39.8491	0.245
1.994-2.055	0.308	136	0.26	2473	0.262	4276	0.941	0.955	61.015	0.24
2.055-2.123	0.263	107	0.248	1903	0.249	4103	0.947	0.956	48.9885	0.218
2.123-2.197	0.285	169	0.221	3720	0.224	3963	0.949	0.967	98.1327	0.188
2.197-2.28	0.235	135	0.212	2389	0.214	3864	0.962	0.97	65.3209	0.174
2.28-2.373	0.237	172	0.18	3535	0.182	3729	0.962	0.978	99.41	0.146
2.373-2.478	0.231	183	0.173	3390	0.176	3598	0.967	0.98	99.3052	0.144
2.478-2.598	0.22	184	0.166	3220	0.169	3411	0.968	0.982	99.7948	0.139
2.598-2.739	0.189	101	0.168	1890	0.169	3260	0.976	0.982	61.0736	0.143
2.739-2.904	0.194	161	0.153	2925	0.155	3108	0.978	0.985	99.2921	0.132
2.904-3.104	0.204	134	0.151	2771	0.153	2925	0.973	0.986	99.3162	0.137
3.104-3.351	0.176	122	0.159	2560	0.159	2706	0.979	0.985	99.1131	0.152
3.351-3.67	0.211	113	0.176	2189	0.178	2531	0.976	0.982	90.9522	0.173
3.67-4.1	0.176	90	0.156	1811	0.157	2288	0.977	0.985	83.0857	0.16
4.1-4.729	0.161	126	0.14	1906	0.141	2055	0.984	0.988	98.8808	0.152
4.729-5.778	0.195	95	0.174	1638	0.175	1737	0.985	0.983	99.7697	0.193
5.778-8.116	0.262	60	0.192	1326	0.195	1395	0.971	0.98	99.3548	0.21
8.116-49.434	0.181	44	0.184	770	0.184	836	0.976	0.976	97.3684	0.23

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