PDB-3grh: Crystal structure of escherichia coli ybhc

ID or keywords:

Entry

Database: PDB / ID: 3grh

Title

Crystal structure of escherichia coli ybhc

Components

Acyl-CoA thioester hydrolase ybgC

Keywords

HYDROLASE / YBHC / BETA-HELIX / PERIPLASMIC / LIPOPROTEIN / OUTER MEMBRANE / E.COLI / CARBOHYDRATE ESTERASE FAMILY 8 / Aspartyl esterase / Cell membrane / Cell outer membrane / Membrane / Palmitate

Function / homology

Function and homology information

pectinesterase activity / : / cell wall modification / Hydrolases; Acting on ester bonds; Thioester hydrolases / carboxylic ester hydrolase activity / cell outer membrane
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.7 Å

Authors

Eklof, J.M. / Tan, T.C. / Divne, C. / Brumer, H.

Citation

Journal: Proteins / Year: 2009
Title: The crystal structure of the outer membrane lipoprotein YbhC from Escherichia coli sheds new light on the phylogeny of carbohydrate esterase family 8.
Authors: Eklof, J.M. / Tan, T.C. / Divne, C. / Brumer, H.

History

Deposition	Mar 25, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 7, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	May 23, 2018	Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3	Dec 11, 2019	Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif Item: _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3grh.cif.gz	93.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3grh.ent.gz	76 KB	Display	PDB format
PDBx/mmJSON format	3grh.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3grh_validation.pdf.gz	433 KB	Display	wwPDB validaton report
Full document	3grh_full_validation.pdf.gz	439.5 KB	Display
Data in XML	3grh_validation.xml.gz	18.4 KB	Display
Data in CIF	3grh_validation.cif.gz	27.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/3grh ftp://data.pdbj.org/pub/pdb/validation_reports/gr/3grh	HTTPS FTP

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Related structure data

Similar structure data	5tzx-1 5tzc-1 5u7j-4 5tzc-3 5tzz-4 5tzw-1 5u7l-1 6c7i-1 5u7k-3 5ahs-3 Search similar-shape structures by Omokage search (details) 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: Acyl-CoA thioester hydrolase ybgC

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

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	79.200, 79.200, 159.650
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

#1: Protein	Acyl-CoA thioester hydrolase ybgC / ybhC Mass: 45956.578 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-399 (UNIPROT RESIDUES 29-427) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b0772, JW0755, ybhC / Plasmid: PNIC28-BSA4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46130
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Acyl-CoA thioester hydrolase ybgC / ybhC

Mass: 45956.578 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-399 (UNIPROT RESIDUES 29-427)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b0772, JW0755, ybhC / Plasmid: PNIC28-BSA4 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46130

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 3.15 Å³/Da / Density % sol: 60.89 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: SODIUM CITRATE, AMMONIUM PHOSPHATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.98 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 27, 2007 / Details: MIRRORS
Radiation	Monochromator: DOUBLE CRYSTAL MONOCHROMATOR, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.98 Å / Relative weight: 1
Reflection	Resolution: 1.7→68 Å / Num. all: 64564 / Num. obs: 64564 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.1 % / R_sym value: 0.118 / Net I/σ(I): 14.2
Reflection shell	Resolution: 1.7→1.8 Å / Redundancy: 9.8 % / Mean I/σ(I) obs: 6.3 / R_sym value: 0.663 / % possible all: 100

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Processing

Software

Name	Version	Classification
ProDC		data collection
SHELXS		phasing
REFMAC	5.2.0019	refinement
XDS		data reduction
XSCALE		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.7→30 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.925 / SU B: 2.617 / SU ML: 0.045 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.084 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.208	1308	2 %	RANDOM
R_work	0.193	-	-	-
all	0.193	63238	-	-
obs	0.193	63238	100 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 13.34 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	-0.03 Å²	0 Å²
2-	-	-0.05 Å²	0 Å²
3-	-	-	0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3044	0	0	243	3287

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.022	0.022	3110
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	2043
X-RAY DIFFRACTION	r_angle_refined_deg	1.874	1.929	4239
X-RAY DIFFRACTION	r_angle_other_deg	1.027	3	4963
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.183	5	395
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.717	24.684	158
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.084	15	464
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.494	15	22
X-RAY DIFFRACTION	r_chiral_restr	0.122	0.2	461
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	3590
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	634
X-RAY DIFFRACTION	r_nbd_refined	0.224	0.2	540
X-RAY DIFFRACTION	r_nbd_other	0.216	0.2	2120
X-RAY DIFFRACTION	r_nbtor_refined	0.188	0.2	1592
X-RAY DIFFRACTION	r_nbtor_other	0.091	0.2	1838
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.156	0.2	169
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.211	0.2	18
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.272	0.2	27
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.151	0.2	7
X-RAY DIFFRACTION	r_mcbond_it	1.816	1.5	2454
X-RAY DIFFRACTION	r_mcbond_other	0.424	1.5	806
X-RAY DIFFRACTION	r_mcangle_it	2.175	2	3172
X-RAY DIFFRACTION	r_scbond_it	3.433	3	1298
X-RAY DIFFRACTION	r_scangle_it	4.758	4.5	1067

LS refinement shell

Resolution: 1.7→1.79 Å / Total num. of bins used: 10

	R_factor	Num. reflection	% reflection
R_free	0.182	212	-
R_work	0.148	9091	-
obs	-	-	99.98 %

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	16.4523	-1.3117	10.4485	0.8507	-2.9129	12.4332	-0.8543	-0.8643	1.0051	0.542	-0.0727	-0.0251	-0.9619	-0.5068	0.9269	0.2341	0.0831	-0.1031	0.0656	-0.0925	0.0203	10.617	47.162	82.908
2	0.9717	-0.8455	-0.6518	2.1026	0.6644	2.4248	-0.0782	-0.049	0.0597	0.3378	0.0607	0.1317	-0.1597	-0.1984	0.0175	0.03	0.0579	-0.0267	0.0794	-0.0031	-0.0052	2.161	40.807	74.158
3	4.2952	-4.0015	0.3038	4.514	-0.3466	2.5668	-0.0594	-0.2073	-0.3498	0.0254	0.1194	0.4372	0.2434	-0.1348	-0.06	0.0415	-0.0197	0.0014	0.0636	0.0291	0.0005	8.915	17.321	73.441
4	7.8864	2.2899	-4.9401	7.9775	-1.9291	11.3936	-0.0696	-0.1272	-0.3865	0.1685	0.0993	-0.578	0.729	1.3075	-0.0297	0.0543	0.1381	0.0108	0.1224	-0.0319	0.0371	34.633	6.821	62.642
5	5.669	2.6414	-2.3552	3.7855	-0.5584	2.9237	-0.0291	-0.0141	-0.2325	0.0306	-0.0312	0.0002	0.3605	0.1209	0.0603	0.1177	0.0013	0.0459	-0.0173	-0.0132	0.0192	21.545	5.478	58.705
6	4.1711	0.7726	-1.1233	1.578	-1.314	2.1481	-0.0823	-0.0628	-0.205	-0.0338	0.04	-0.1844	0.2397	0.2358	0.0423	0.0334	0.0491	0.0139	0.038	-0.0392	-0.0023	29.563	13.405	63.524
7	0.7064	0.1447	-0.2844	0.9489	-0.2094	2.4294	-0.0509	0.0763	-0.0828	-0.0996	0.0776	-0.0902	0.0727	0.1509	-0.0267	0.0238	0.0131	0.0265	0.035	-0.0072	-0.003	25.887	19.462	58.269
8	2.3203	1.2834	1.0674	2.6584	-0.8286	5.0904	0.0254	0.3031	-0.1117	-0.3077	0.0183	-0.1581	0.2859	0.0092	-0.0437	0.1213	-0.0303	0.0358	0.0278	-0.0205	-0.0482	22.306	14.967	44.347
9	3.0077	-1.9314	5.2442	7.1685	-5.4775	10.6346	-0.0035	0.3192	-0.0358	-0.5697	0.0064	0.1417	0.3265	0.1825	-0.0029	0.0996	-0.0234	0.0357	0.1096	0.0119	-0.004	18.697	25.229	45.615
10	0.8787	-0.0012	-0.2917	0.4738	-0.1115	1.1088	-0.0287	0.0815	0.0244	-0.056	0.0549	-0.0558	0.0213	0.0143	-0.0263	0.0357	-0.0062	0.0138	0.0471	0.0019	0.019	21.467	25.697	59.174
11	5.5321	0.6502	0.8925	1.9106	0.4396	1.4882	0.0608	0.306	-0.0752	-0.2599	-0.0167	-0.0327	0.0164	-0.1454	-0.0442	0.0563	-0.0144	0.0006	0.0791	0.0024	-0.0032	9.795	22.9	53.371
12	0.6357	-0.4023	0.0142	0.3391	-0.2659	1.0766	-0.0102	0.0213	-0.009	-0.0466	0.0221	-0.0289	-0.0063	-0.0708	-0.0119	0.0442	0.004	-0.0035	0.0422	-0.0034	0.0237	13.109	28.046	63.288
13	2.7189	1.8688	-3.5109	3.7318	-4.9411	8.3928	0.1195	-0.0307	0.237	0.154	-0.1006	-0.103	-0.314	0.3128	-0.019	0.0458	-0.0296	0.0126	0.0161	-0.005	0.0549	23.433	39.68	62.627
14	1.6021	-0.4224	0.3876	0.8089	-0.04	0.3456	-0.0252	-0.001	-0.0436	-0.039	0.0969	0.0539	-0.0542	-0.1216	-0.0717	0.0433	0.0143	-0.0115	0.0434	0.0042	0.0245	7.429	33.48	64.672
15	2.5502	-0.0092	1.5057	1.1485	-0.5656	3.2589	-0.0018	0.137	0.3582	-0.1221	-0.0482	-0.1767	-0.1171	0.0748	0.05	0.0659	0.0034	0.0059	0.0146	0.0018	0.0292	16.223	41.839	61.908
16	3.1339	0.9712	2.7595	1.7367	2.0728	3.6587	-0.1663	0.0812	0.1682	-0.1217	0.1687	-0.0205	-0.2924	-0.0088	-0.0025	0.0592	0.025	-0.0265	0.0449	-0.0015	0.0176	9.513	38.323	68.001
17	4.8667	-0.1975	-0.7977	1.2092	-0.8215	0.7377	0.0681	0.0207	0.4832	-0.1288	-0.0198	-0.1031	-0.2114	-0.1996	-0.0482	0.0869	0.0264	-0.0184	0.0197	0.0261	0.0144	7.627	46.171	60.622
18	7.1126	0.053	1.2036	20.052	8.0702	15.4783	0.3323	-1.0277	0.3165	2.0798	-1.0636	1.8551	-0.0762	-1.9845	0.7313	0.2869	0.0466	0.204	0.4303	-0.0933	0.1059	-9.38	46.105	76.67
19	1.9802	-0.3919	1.2091	0.7146	-0.9086	3.1716	-0.1044	-0.0029	0.0883	0.0074	0.0507	0.0208	-0.0489	-0.1544	0.0538	0.038	0.0407	-0.0366	0.0568	0.0038	0.0277	-0.552	40.651	64.765
20	12.3443	3.3974	-3.4172	2.0988	-0.2623	5.5012	0.2067	-0.423	0.7465	0.5095	0.118	0.0496	-0.4523	0.0856	-0.3247	0.0834	0.0412	-0.048	0.0149	-0.0697	0.0507	13.537	44.848	77.07

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 27
3	X-RAY DIFFRACTION	3	A	28 - 51
4	X-RAY DIFFRACTION	4	A	52 - 67
5	X-RAY DIFFRACTION	5	A	68 - 83
6	X-RAY DIFFRACTION	6	A	84 - 95
7	X-RAY DIFFRACTION	7	A	96 - 132
8	X-RAY DIFFRACTION	8	A	133 - 160
9	X-RAY DIFFRACTION	9	A	161 - 173
10	X-RAY DIFFRACTION	10	A	174 - 225
11	X-RAY DIFFRACTION	11	A	226 - 237
12	X-RAY DIFFRACTION	12	A	238 - 267
13	X-RAY DIFFRACTION	13	A	268 - 282
14	X-RAY DIFFRACTION	14	A	283 - 303
15	X-RAY DIFFRACTION	15	A	304 - 322
16	X-RAY DIFFRACTION	16	A	323 - 338
17	X-RAY DIFFRACTION	17	A	339 - 361
18	X-RAY DIFFRACTION	18	A	362 - 372
19	X-RAY DIFFRACTION	19	A	373 - 383
20	X-RAY DIFFRACTION	20	A	384 - 392

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