PDB-8gld: Crystal structure of the peptidoglycan O-acetylesterase Ape1 (ami...

ID or keywords:

Entry

Database: PDB / ID: 8gld

Title

Crystal structure of the peptidoglycan O-acetylesterase Ape1 (amino acids 22-392) from Campylobacter jejuni

Components

SGNH hydrolase-type esterase domain-containing protein

Keywords

HYDROLASE / Peptidoglycan O-acetylesterase / SGNH hydrolase / CBM35 / product bound complex

Function / homology

SGNH hydrolase-type esterase domain / GDSL-like Lipase/Acylhydrolase family / SGNH hydrolase superfamily /

ACETATE ION / SGNH hydrolase-type esterase domain-containing protein

Function and homology information

Biological species

Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.3 Å

Authors

Lin, C.S. / Murphy, M.E.

Funding support

Canada, 1items

Citation

Journal: To be published
Title: Mechanism of the CBM35 domain in assisting catalysis by Ape1, a Campylobacter jejuni O-acetyl esterase
Authors: Lin, C.S. / Yen, I.Y. / Chan, A.C. / Murphy, M.E.

History

Deposition	Mar 22, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 27, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8gld.cif.gz	448.7 KB	Display	PDBx/mmCIF format
PDB format	pdb8gld.ent.gz	368.8 KB	Display	PDB format
PDBx/mmJSON format	8gld.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gl/8gld ftp://data.pdbj.org/pub/pdb/validation_reports/gl/8gld	HTTPS FTP

-
Related structure data

Related structure data	8gkdC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: SGNH hydrolase-type esterase domain-containing protein

B: SGNH hydrolase-type esterase domain-containing protein

C: SGNH hydrolase-type esterase domain-containing protein

hetero molecules

130 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: SGNH hydrolase-type esterase domain-containing protein

hetero molecules

defined by author
Evidence: gel filtration
43.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: SGNH hydrolase-type esterase domain-containing protein

hetero molecules

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

3

C: SGNH hydrolase-type esterase domain-containing protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	95.311, 95.311, 103.034
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	145
Space group name H-M	P3₂

#1: Protein	SGNH hydrolase-type esterase domain-containing protein Mass: 43192.598 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni subsp. jejuni 81-176 (Campylobacter) Strain: 81-176 / Gene: CJJ81176_0638 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H3PJ52
#2: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.09 Å³/Da / Density % sol: 41.01 % / Description: rod-shaped crystal
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 166 mM sodium acetate, 28% (w/v) PEG4000, and 80 mM Tris-HCl pH8.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

CLSI

/ Beamline: 08ID-1 / Wavelength: 0.98 Å

Detector

Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 1, 2016

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection twin

Operator: -h,-k,l / Fraction: 0.38

Reflection

Resolution: 2.3→50 Å / Num. obs: 46459 / % possible obs: 100 % / Redundancy: 5.8 % / R_merge(I) obs: 0.148 / R_pim(I) all: 0.067 / R_rim(I) all: 0.163 / Χ²: 1.081 / Net I/σ(I): 5.4

Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique obs	CC_1/2	CC star	R_pim(I) all	R_rim(I) all	Χ²
2.3-2.34	5.8	0.782	2322	0.653	0.889	0.356	0.86	0.876
2.34-2.38	5.8	0.741	2331	0.705	0.909	0.338	0.815	0.917
2.38-2.43	5.8	0.689	2320	0.727	0.917	0.314	0.758	0.92
2.43-2.48	5.8	0.559	2273	0.826	0.951	0.255	0.615	0.935
2.48-2.53	5.8	0.521	2321	0.851	0.959	0.237	0.572	0.965
2.53-2.59	5.8	0.509	2360	0.825	0.951	0.232	0.56	0.966
2.59-2.66	5.8	0.446	2326	0.881	0.968	0.203	0.49	0.979
2.66-2.73	5.8	0.4	2312	0.891	0.971	0.182	0.439	1.104
2.73-2.81	5.8	0.353	2367	0.9	0.973	0.16	0.388	1.007
2.81-2.9	5.8	0.315	2280	0.918	0.979	0.143	0.346	1.062
2.9-3	5.8	0.254	2327	0.94	0.984	0.115	0.279	1.112
3-3.12	5.8	0.202	2315	0.962	0.99	0.092	0.222	1.14
3.12-3.26	5.9	0.155	2339	0.976	0.994	0.07	0.17	1.171
3.26-3.44	5.9	0.129	2318	0.982	0.995	0.059	0.142	1.244
3.44-3.65	5.8	0.107	2317	0.988	0.997	0.048	0.117	1.259
3.65-3.93	5.8	0.089	2315	0.991	0.998	0.04	0.097	1.231
3.93-4.33	5.9	0.069	2359	0.994	0.999	0.031	0.076	1.181
4.33-4.95	5.9	0.06	2296	0.995	0.999	0.027	0.066	1.292
4.95-6.24	5.9	0.064	2315	0.995	0.999	0.029	0.07	1.091
6.24-50	5.9	0.048	2346	0.998	0.999	0.021	0.052	1.162

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.3 Å	43.7 Å
Translation	2.3 Å	43.7 Å

-
Processing

Software

Name	Version	Classification
PHENIX	1.17.1	refinement
SCALEPACK		data scaling
PHASER	2.5.6	phasing
PDB_EXTRACT	3.27	data extraction
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.3→43.7 Å / Cross valid method: THROUGHOUT / σ(F): 169.8 / Phase error: 24.64 / Stereochemistry target values: TWIN_LSQ_F

	R_factor	Num. reflection	% reflection
R_free	0.1797	1993	4.29 %
R_work	0.1518	-	-
obs	0.1568	46431	99.96 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.3→43.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8870	0	12	355	9237

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	9053
X-RAY DIFFRACTION	f_angle_d	0.515	12185
X-RAY DIFFRACTION	f_dihedral_angle_d	5.498	1164
X-RAY DIFFRACTION	f_chiral_restr	0.041	1341
X-RAY DIFFRACTION	f_plane_restr	0.003	1542

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.3-2.38	0.2985	198	0.2888	4454	X-RAY DIFFRACTION	99.6
2.38-2.48	0.3296	185	0.2809	4399	X-RAY DIFFRACTION	100
2.48-2.59	0.2987	193	0.2815	4485	X-RAY DIFFRACTION	99.9
2.59-2.73	0.3027	200	0.2813	4443	X-RAY DIFFRACTION	100
2.73-2.9	0.2879	210	0.2779	4431	X-RAY DIFFRACTION	100
2.9-3.12	0.3212	198	0.2613	4446	X-RAY DIFFRACTION	100
3.12-3.44	0.298	204	0.2627	4447	X-RAY DIFFRACTION	100
3.44-3.93	0.256	194	0.2453	4440	X-RAY DIFFRACTION	100
3.93-4.95	0.2601	197	0.2406	4448	X-RAY DIFFRACTION	100
4.95-43.7	0.2764	214	0.2565	4441	X-RAY DIFFRACTION	100

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	1.9482	-0.1542	-0.2843	1.7709	0.8492	5.8281	0.0421	0.0172	-0.0918	-0.2607	0.294	-0.2979	0.2013	0.7888	-0.2629	0.2413	-0.0121	0.0144	0.2946	-0.0296	0.2626	70.6273	-29.1369	5.4873
2	0.9049	0.0506	-0.3634	1.2971	-0.0645	0.4745	0.022	-0.019	-0.0536	-0.0382	-0.0058	-0.0987	0.1736	0.0635	-0.013	0.2311	-0.0007	-0.0041	0.2395	-0.029	0.0807	52.0805	-33.5714	11.4104
3	1.0958	-0.4738	0.3571	1.1577	0.3614	1.0057	0.0102	0.0557	0.1133	-0.2683	0.0845	0.0155	-0.2204	-0.1451	-0.0846	0.3024	-0.0238	0.0412	0.2898	0.0262	0.1236	34.8909	-19.9686	10.0078
4	1.6657	0.3241	-0.7578	1.1336	0.3327	1.2257	0.1439	0.1466	-0.0576	-0.0471	-0.0688	0.1553	0.1329	-0.2386	-0.0655	0.2347	-0.0209	-0.0141	0.2867	0.0119	0.1071	28.6049	-33.2062	14.5376
5	0.5078	0.1216	-0.181	0.6528	-0.0162	0.6372	-0.0349	0.0851	0.0066	0.0501	0.098	0.0789	0.0804	-0.0235	-0.0432	0.2446	-0.0107	-0.0148	0.1962	0.0005	0.0996	41.2362	-28.4394	16.7549
6	0.6147	0.744	-0.6564	1.5702	-0.3684	1.1714	0.0829	-0.065	0.1099	0.2449	-0.0221	0.0333	-0.3188	0.0178	-0.0391	0.2883	0.0118	-0.0075	0.2065	-0.0364	0.1301	54.4751	-14.8133	20.4364
7	1.6147	0.5268	-0.5115	0.9335	0.6578	2.1324	0.015	0.151	0.1818	-0.2318	0.0729	0.0547	-0.4584	0.1032	0.0135	0.252	0.0171	-0.0162	0.2487	-0.0329	0.1432	59.0152	-15.4084	8.4642
8	1.128	0.3781	-0.1891	1.0833	-0.3856	1.0648	-0.0223	0.0542	-0.0077	-0.0053	0.026	-0.1575	-0.085	0.1119	0.0055	0.2178	-0.044	0.016	0.2734	-0.0427	0.1185	64.1948	-21.939	6.7002
9	1.2768	0.2584	-1.3302	1.262	-0.2412	6.7312	0.2572	-0.3692	0.0206	0.1473	-0.1219	0.2082	-0.7926	-0.7044	-0.1917	0.3306	0.0444	0.0383	0.3742	0.0442	0.2805	-12.8498	-35.9383	31.352
10	0.9564	-0.021	-0.0741	1.2376	0.093	0.9521	-0.0238	-0.0037	-0.0033	0.009	0.0428	0.1228	0.0506	-0.2505	-0.0261	0.2283	-0.0062	0.029	0.2528	0.0059	0.0911	-7.4064	-54.3162	25.635
11	0.8782	0.0308	-0.1093	1.3725	0.0838	0.6582	-0.0062	-0.135	-0.073	0.1424	0.067	-0.0761	0.1959	0.1211	-0.0505	0.3056	0.015	-0.0221	0.2475	-0.0094	0.094	8.4555	-68.8078	25.8681
12	1.4384	-0.8314	-1.1005	1.276	0.0995	0.8311	0.0521	0.2503	-0.2848	-0.0624	-0.0461	0.0332	0.1219	-0.1602	0.0238	0.3118	-0.0015	-0.0299	0.2589	-0.011	0.0862	1.9817	-72.1122	21.3109
13	0.2196	-0.1056	-0.4087	0.5407	-0.1958	1.0533	-0.097	0.0164	-0.0229	0.0494	0.0511	-0.0446	-0.0157	0.0258	0.0327	0.2028	-0.0157	-0.0056	0.2186	0.0263	0.0964	4.239	-54.0465	16.9621
14	0.4901	0.7302	0.3033	1.6824	0.2254	1.501	0.0122	0.1754	0.0864	-0.0612	0.0812	-0.0171	-0.2187	0.2101	-0.1221	0.2582	0.0053	0.036	0.2698	0.0177	0.1366	7.6932	-42.8568	16.6723
15	1.0839	0.0679	-0.4892	1.4346	0.3927	1.178	-0.092	-0.0348	0.1443	-0.1143	0.1344	-0.0331	-0.5629	0.1956	-0.0479	0.3525	-0.0243	0.0363	0.2174	0.0243	0.1234	1.841	-36.7159	25.4563
16	0.6751	0.0272	0.7544	0.9093	-0.3697	1.0023	0.0337	-0.1949	0.0808	0.2032	0.0025	0.1243	-0.1301	-0.1745	-0.0224	0.3236	0.0155	0.0549	0.2563	-0.0048	0.1326	-5.8411	-40.5828	35.9567
17	1.1435	0.0073	1.5932	1.8488	0.2789	7.7607	0.3697	-0.3999	-0.1886	0.6049	0.2975	-0.3454	0.6819	0.0647	-0.681	0.6454	0.0564	-0.1127	0.5107	-0.0266	0.4396	2.997	-21.927	17.6989
18	1.0731	0.5097	0.2255	1.2242	-0.2233	1.3765	-0.0223	0.0385	0.0138	0.1078	-0.0184	-0.0648	0.002	0.3195	0.0516	0.3085	-0.0218	-0.0065	0.378	0.0351	0.1659	1.9311	0.9018	12.0798
19	1.0885	0.455	0.4362	0.9083	-0.1072	1.1103	-0.1101	-0.2144	0.1137	-0.1419	-0.0494	-0.1927	-0.4317	0	0.0742	0.4367	-0.0663	-0.0182	0.356	-0.0237	0.2351	3.3508	16.2813	16.6147
20	1.8602	-0.0303	-0.4322	1.4693	0.0371	1.1662	0.1505	0.1058	0.3909	-0.096	-0.1649	-0.0244	-0.472	0.2843	-0.007	0.6754	-0.0844	-0.0265	0.3757	-0.0038	0.3141	5.2438	20.8123	5.7642
21	1.28	-0.514	0.7005	3.0124	-0.1086	1.3203	-0.0637	0.0231	0.2607	0.3323	-0.064	-0.2699	-0.1723	0.3053	0.113	0.424	-0.0656	-0.0416	0.3638	0.0304	0.1848	5.5072	12.2049	9.978
22	1.2515	0.0391	0.0424	0.8396	-0.0288	0.6479	0.0156	0.1068	0.0925	-0.0261	-0.0578	0.0306	-0.0449	0.1123	0.0092	0.3599	-0.0094	-0.0312	0.3218	-0.0086	0.1528	-4.3481	1.1699	3.081
23	1.3854	0.3331	0.1781	1.2574	-0.408	1.4759	0.03	0.0566	0.0185	-0.0657	-0.0879	0.1219	0.2499	-0.3238	0.0276	0.3504	-0.024	-0.0015	0.3618	-0.0335	0.185	-12.2893	-11.217	7.5684
24	1.2948	0.5393	0.4548	1.4893	0.4267	0.8933	-0.0215	-0.14	-0.2464	0.1917	-0.066	-0.0431	0.1888	0.2769	0.101	0.4369	0.0306	0.0074	0.3255	0.0419	0.2258	-2.295	-16.4934	19.1887

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 28 through 48 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 49 through 109 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 110 through 136 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 137 through 202 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 203 through 266 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 267 through 296 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 297 through 321 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 322 through 392 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 28 through 48 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 49 through 109 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 110 through 177 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 178 through 234 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 235 through 266 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 267 through 296 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 297 through 351 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 352 through 392 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 28 through 48 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 49 through 136 )
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 137 through 157 )
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 158 through 202 )
21	X-RAY DIFFRACTION	21	chain 'C' and (resid 203 through 234 )
22	X-RAY DIFFRACTION	22	chain 'C' and (resid 235 through 266 )
23	X-RAY DIFFRACTION	23	chain 'C' and (resid 267 through 337 )
24	X-RAY DIFFRACTION	24	chain 'C' and (resid 338 through 392 )

-
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

-
Phasing

-
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

-Phasing

-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

-
Phasing

-
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