PDB-9otj: Crystal Structure of Salmonella FraB Deglycase, Crystal Form 1

ID or keywords:

Entry

Database: PDB / ID: 9otj

Title

Crystal Structure of Salmonella FraB Deglycase, Crystal Form 1

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: 1.851 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

-
Download

PDBx/mmCIF format	9otj.cif.gz	144.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9otj.ent.gz	107.3 KB	Display	PDB format
PDBx/mmJSON format	9otj.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9otj_validation.pdf.gz	440.8 KB	Display	wwPDB validaton report
Full document	9otj_full_validation.pdf.gz	455.2 KB	Display
Data in XML	9otj_validation.xml.gz	31.5 KB	Display
Data in CIF	9otj_validation.cif.gz	42 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ot/9otj ftp://data.pdbj.org/pub/pdb/validation_reports/ot/9otj	HTTPS FTP

-
Related structure data

Related structure data	9otlC 9otrC 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

-
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, AB dimer is present in asymmetric unit. Dimer is observed by native mass spectrometry.

Unit cell

Length a, b, c (Å)	55.292, 108.515, 120.856
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.: 273 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.34 Å³/Da / Density % sol: 47.39 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 15% v/v 2-propanol, 0.1 M magnesium chloride, 0.1 M MES, pH 6.5

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 5, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9793 Å / Relative weight: 1
Reflection	Resolution: 1.85→80.743 Å / Num. obs: 53947 / % possible obs: 86 % / Redundancy: 6.3 % / R_merge(I) obs: 0.049 / R_pim(I) all: 0.021 / Net I/σ(I): 16.1
Reflection shell	Resolution: 1.851→1.975 Å / Redundancy: 6.9 % / R_merge(I) obs: 1.57 / Num. unique obs: 2697 / R_pim(I) all: 0.648 / % possible all: 24.7

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0430	refinement
XDS	Jan 26, 2018 (BUILT 20180808)	data reduction
Aimless	0.7.4	data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.851→80.743 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.941 / SU B: 5.964 / SU ML: 0.154 / Cross valid method: FREE R-VALUE / ESU R: 0.157 / ESU R Free: 0.158
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2538	2620	4.869 %
R_work	0.1955	51194	-
all	0.198	-	-
obs	-	53814	85.724 %

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: 50.417 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.032 Å²	0 Å²	-0 Å²
2-	-	-0.224 Å²	0 Å²
3-	-	-	0.191 Å²

Refinement step

Cycle: LAST / Resolution: 1.851→80.743 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4801	0	0	273	5074

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.012	4917
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4491
X-RAY DIFFRACTION	r_angle_refined_deg	1.96	1.799	6675
X-RAY DIFFRACTION	r_angle_other_deg	0.66	1.737	10297
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.135	5	617
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	14.375	5	19
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	16.88	10	751
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.412	10	230
X-RAY DIFFRACTION	r_chiral_restr	0.1	0.2	726
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5854
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1184
X-RAY DIFFRACTION	r_nbd_refined	0.229	0.2	1159
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	4365
X-RAY DIFFRACTION	r_nbtor_refined	0.193	0.2	2473
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.086	0.2	2733
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.2	0.2	279
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.084	0.2	1
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.268	0.2	5
X-RAY DIFFRACTION	r_nbd_other	0.231	0.2	33
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.191	0.2	9
X-RAY DIFFRACTION	r_mcbond_it	5.467	5.115	2480
X-RAY DIFFRACTION	r_mcbond_other	5.464	5.115	2480
X-RAY DIFFRACTION	r_mcangle_it	7.486	9.172	3093
X-RAY DIFFRACTION	r_mcangle_other	7.485	9.174	3094
X-RAY DIFFRACTION	r_scbond_it	6.163	5.799	2437
X-RAY DIFFRACTION	r_scbond_other	6.161	5.8	2438
X-RAY DIFFRACTION	r_scangle_it	8.736	10.398	3582
X-RAY DIFFRACTION	r_scangle_other	8.735	10.399	3583
X-RAY DIFFRACTION	r_lrange_it	11.348	51.666	5777
X-RAY DIFFRACTION	r_lrange_other	11.305	51.414	5714

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
1.851-1.899	0.286	9	0.443	94	0.428	4586	0.869	0.794	2.246	0.436
1.899-1.951	0.482	48	0.456	1210	0.457	4446	0.818	0.794	28.2951	0.474
1.951-2.008	0.4	181	0.334	3358	0.338	4343	0.908	0.923	81.4874	0.331
2.008-2.07	0.41	210	0.399	3952	0.4	4236	0.82	0.855	98.2531	0.401
2.07-2.137	0.383	195	0.312	3878	0.315	4098	0.896	0.924	99.3899	0.293
2.137-2.212	0.313	200	0.252	3787	0.255	3993	0.933	0.955	99.8497	0.226
2.212-2.296	0.46	179	0.418	3435	0.42	3803	0.835	0.846	95.0302	0.387
2.296-2.389	0.285	181	0.262	3502	0.263	3692	0.94	0.952	99.7562	0.226
2.389-2.496	0.303	183	0.211	3362	0.216	3553	0.941	0.972	99.7748	0.18
2.496-2.617	0.259	152	0.184	3223	0.188	3382	0.964	0.979	99.793	0.158
2.617-2.759	0.271	164	0.188	3079	0.192	3260	0.957	0.979	99.4785	0.167
2.759-2.926	0.289	141	0.181	2902	0.186	3062	0.946	0.98	99.3795	0.17
2.926-3.127	0.214	159	0.172	2709	0.174	2877	0.971	0.982	99.6872	0.17
3.127-3.378	0.245	112	0.189	2591	0.192	2710	0.965	0.981	99.7417	0.194
3.378-3.699	0.238	120	0.191	2373	0.194	2515	0.968	0.981	99.1253	0.199
3.699-4.135	0.179	99	0.154	2137	0.155	2254	0.98	0.986	99.2014	0.172
4.135-4.773	0.185	105	0.127	1900	0.13	2030	0.978	0.99	98.7685	0.156
4.773-5.84	0.197	85	0.147	1635	0.149	1732	0.98	0.988	99.3072	0.18
5.84-8.238	0.262	53	0.18	1309	0.183	1379	0.965	0.98	98.7672	0.22
8.238-80.743	0.294	44	0.195	758	0.2	816	0.936	0.97	98.2843	0.333

-
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