PDB-3aag: Crystal structure of C. jejuni pglb C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 3aag

Title

Crystal structure of C. jejuni pglb C-terminal domain

Components

General glycosylation pathway protein

Keywords

TRANSFERASE / MULTIDOMAIN

Function / homology

Function and homology information

undecaprenyl-diphosphooligosaccharide-protein glycotransferase /

oligosaccharyl transferase activity / protein N-linked glycosylation /

glycosyltransferase activity / membrane => GO:0016020 /

metal ion binding /

plasma membrane
Similarity search - Function

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.8 Å

Authors

Maita, N. / Kohda, D.

Citation

Journal: J.Biol.Chem. / Year: 2010
Title: Comparative structural biology of Eubacterial and Archaeal oligosaccharyltransferases.
Authors: Maita, N. / Nyirenda, J. / Igura, M. / Kamishikiryo, J. / Kohda, D.

History

Deposition	Nov 16, 2009	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Dec 8, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	3aag.cif.gz	111 KB	Display	PDBx/mmCIF format
PDB format	pdb3aag.ent.gz	95.1 KB	Display	PDB format
PDBx/mmJSON format	3aag.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/aa/3aag ftp://data.pdbj.org/pub/pdb/validation_reports/aa/3aag	HTTPS FTP

-
Related structure data

Similar structure data	5ytu-4 2c6e-1 4rsm-4 2c3j-d 5jzj-2 5n9s-d 1w69-d 2bhh-d 4x7n-d 1ik6-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#266 - Feb 2022 Oligosaccharyltransferase similarity (5)

Deposited unit

A: General glycosylation pathway protein

B: General glycosylation pathway protein

hetero molecules

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

1

A: General glycosylation pathway protein

hetero molecules

defined by author&software
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: General glycosylation pathway protein

defined by author&software
34.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	115.258, 115.258, 88.883
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	172
Space group name H-M	P6₄

#1: Protein	General glycosylation pathway protein Mass: 34204.945 Da / Num. of mol.: 2 / Fragment: PGLB C-TERMINAL DOMAIN / Mutation: OLIGOSACCHARYLTRANSFERASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: RM1221 / Gene: CJE1268, pglB / Plasmid: PGEX6P / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HTX9
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

#1: Protein

General glycosylation pathway protein

Mass: 34204.945 Da / Num. of mol.: 2 / Fragment: PGLB C-TERMINAL DOMAIN / Mutation: OLIGOSACCHARYLTRANSFERASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Campylobacter jejuni (Campylobacter) / Strain: RM1221 / Gene: CJE1268, pglB / Plasmid: PGEX6P / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HTX9

#2: Chemical

ChemComp-CA / CALCIUM ION

Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 18% PEG 8000, 0.2M CALCIUM ACETATE, 0.1M SODIUM CACODYLATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	SPring-8	BL44XU	1	1.1
SYNCHROTRON	SPring-8	BL38B1	2	0.97881, 0.97909, 0.9400

Detector

Type	ID	Detector	Date	Details
Bruker DIP-6040	1	CCD	Jul 4, 2007	mirrors
RIGAKU JUPITER 210	2	CCD	Jun 21, 2007	mirrors

Radiation

ID	Monochromator	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	Si	SINGLE WAVELENGTH	M	x-ray	1
2	Si	MAD	M	x-ray	1

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	1.1	1
2	0.97881	1
3	0.97909	1
4	0.94	1

Reflection

Resolution: 2.8→30 Å / Num. all: 16621 / Num. obs: 16601 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / B_iso Wilson estimate: 68.9 Å² / R_sym value: 0.085 / Net I/σ(I): 9.3

Reflection shell

Resolution: 2.8→2.9 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.37 / Num. unique all: 1651 / R_sym value: 0.503 / % possible all: 100

-
Processing

Software

Name	Version	Classification
HKL-2000		data collection
SHARP		phasing
REFMAC	5.5.0104	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.8→20 Å / Cor.coef. F_o:F_c: 0.908 / Cor.coef. F_o:F_c free: 0.909 / SU B: 33.155 / SU ML: 0.298 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(I): 3 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26006	1276	7.7 %	RANDOM
R_work	0.24511	-	-	-
obs	0.24626	15279	99.91 %	-
all	-	15293	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 33.286 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.14 Å²	-0.07 Å²	0 Å²
2-	-	-0.14 Å²	0 Å²
3-	-	-	0.21 Å²

Refinement step

Cycle: LAST / Resolution: 2.8→20 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4035	0	1	0	4036

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.002	0.022	4129
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.335	1.974	5600
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.623	5	495
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.655	24.392	189
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.258	15	593
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.154	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.03	0.2	633
X-RAY DIFFRACTION	r_gen_planes_refined	0.001	0.021	3108
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.269	1.5	2509
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.495	2	4043
X-RAY DIFFRACTION	r_scbond_it	0.434	3	1620
X-RAY DIFFRACTION	r_scangle_it	0.701	4.5	1557
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.801→2.873 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.333	94	-
R_work	0.321	1120	-
obs	-	1214	99.67 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	4.6503	-0.5647	0.3369	7.9924	2.9133	5.6435	-0.3731	-0.3649	0.539	-0.1456	0.0705	0.0185	-0.2125	-0.0331	0.3026	0.328	-0.0096	-0.0396	0.3064	-0.0261	0.3519	-44.1845	35.7798	14.9904
2	1.7407	-0.6621	0.4295	1.6281	-0.2569	2.7272	0.0039	-0.0049	0.0379	-0.0003	0.1029	-0.0613	0.0289	-0.0216	-0.1069	0.2997	-0.0021	-0.0277	0.291	-0.0188	0.3031	-46.8159	25.9634	12.6579
3	1.8026	-0.6118	0.1436	2.1324	0.5935	1.3666	-0.1585	0.1864	-0.2648	0.2056	0.1133	0.21	0.1221	-0.1363	0.0452	0.3538	-0.0084	0.012	0.3107	-0.0355	0.3218	-45.5647	17.4789	12.3298
4	2.8952	-1.3039	-0.3268	3.7208	1.9981	1.1316	0.0278	0.2837	-0.0615	-0.1106	0.0248	-0.0984	-0.0512	0.0689	-0.0527	0.3215	-0.0087	0.0105	0.4222	-0.0367	0.3208	-39.7281	17.5911	1.2783
5	3.9619	-1.6265	-0.5383	7.6288	1.4234	1.1207	-0.1782	0.388	-0.656	0.0707	0.1687	1.0206	0.3916	-0.092	0.0094	0.3595	-0.0177	-0.0296	0.3816	-0.1198	0.3902	-47.5353	7.2894	-0.4442
6	2.6358	-0.0384	-0.1541	2.073	0.39	0.0882	-0.0084	0.3829	-0.0386	-0.21	0.0479	-0.2505	0.0054	-0.014	-0.0395	0.3255	-0.0018	0.0119	0.3744	-0.0679	0.3005	-38.0675	19.0561	4.4221
7	5.1566	0.8557	2.8444	0.8093	0.6197	4.9675	0.159	-0.1376	-0.2185	0.3981	0.0516	-0.3607	0.67	0.0933	-0.2106	0.352	0.0756	-0.2269	0.3604	-0.0941	0.4819	-18.5932	17.6103	22.3275
8	6.3535	0.8572	-1.2352	1.7315	0.6795	2.4055	-0.2954	0.3795	0.5726	0.0851	0.2103	-0.9918	-0.1794	1.0999	0.0851	0.0767	-0.1844	-0.2495	0.8826	0.2983	1.1695	-13.241	23.4123	13.3501
9	3.2339	1.2104	0.2715	3.4997	-2.419	2.8788	0.0013	0.3413	-0.1238	0.3699	-0.2756	-0.6287	0.0485	0.2478	0.2744	0.2794	0.0251	-0.1446	0.449	-0.0603	0.4304	-20.9487	22.5173	15.222
10	4.1285	-1.2477	0.1793	4.2793	0.7725	3.8177	-0.0997	0.3706	0.512	-0.2493	0.1436	-0.4146	-0.2861	0.2304	-0.0439	0.2781	-0.0784	0.0401	0.3259	0.0149	0.3477	-32.9969	29.8046	4.7278
11	9.1397	2.9773	2.2599	2.3642	0.0381	7.5231	-0.2289	-0.4254	-0.2252	-0.0956	0.0082	-0.5087	-0.6734	0.1092	0.2207	0.4658	0.2692	-0.276	0.3247	-0.1449	0.4587	-21.4711	15.2114	39.9639
12	4.4721	2.2451	1.0163	2.269	1.927	1.9967	0.0302	0.0442	-1.1791	0.2454	0.2209	-0.6121	0.272	0.2832	-0.2511	0.569	0.3013	-0.2279	0.337	0.049	0.5722	-27.4013	6.8321	35.586
13	1.6593	-0.8868	0.6671	2.7449	-0.6274	0.7796	-0.032	-0.2991	-0.5181	0.2695	0.0691	-0.044	0.2893	0.2139	-0.0371	0.638	0.3063	-0.2443	0.3834	0.123	0.4988	-31.0651	3.0486	45.1893
14	4.5472	-2.5523	1.2513	2.665	0.5348	1.5932	-0.0959	-0.1121	-0.3407	0.3089	0.1331	0.2077	0.2084	0.0326	-0.0373	0.4052	0.0457	-0.0115	0.3445	-0.0312	0.2824	-49	21.6738	30.7228
15	5.0621	-1.3101	-2.5785	3.6403	-1.6382	2.9616	-0.3883	-0.375	-0.1927	0.5281	0.5416	0.3696	0.0425	-0.115	-0.1532	0.6366	0.1511	-0.0143	0.284	0.0863	0.2003	-52.245	21.5957	41.2805
16	3.2584	-2.1125	0.1942	2.9483	1.5247	1.7605	-0.351	-0.4638	-0.0975	0.433	0.3932	0.0092	0.0851	0.0426	-0.0421	0.5716	0.1779	-0.1241	0.4248	0.0508	0.2205	-41.4978	18.8564	41.829
17	2.6608	-3.1376	-4.4543	3.9813	5.6398	7.9896	-0.3172	-1.2806	0.2667	0.11	0.9196	-0.3306	0.1643	1.5114	-0.6024	0.6763	0.1361	-0.4819	1.3928	-0.0029	0.3825	-30.1797	17.9388	47.5354

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	436 - 445
2	X-RAY DIFFRACTION	2	A	446 - 466
3	X-RAY DIFFRACTION	3	A	467 - 489
4	X-RAY DIFFRACTION	4	A	490 - 509
5	X-RAY DIFFRACTION	5	A	510 - 540
6	X-RAY DIFFRACTION	6	A	541 - 578
7	X-RAY DIFFRACTION	7	A	579 - 616
8	X-RAY DIFFRACTION	8	A	617 - 653
9	X-RAY DIFFRACTION	9	A	654 - 682
10	X-RAY DIFFRACTION	10	A	683 - 713
11	X-RAY DIFFRACTION	11	B	436 - 466
12	X-RAY DIFFRACTION	12	B	467 - 493
13	X-RAY DIFFRACTION	13	B	494 - 570
14	X-RAY DIFFRACTION	14	B	571 - 621
15	X-RAY DIFFRACTION	15	B	622 - 658
16	X-RAY DIFFRACTION	16	B	659 - 700
17	X-RAY DIFFRACTION	17	B	701 - 713

-
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