PDB-9grb: Crystal structure of mouse Carboxylesterase 2b (Ces2b)

ID or keywords:

Entry

Database: PDB / ID: 9grb

Title

Crystal structure of mouse Carboxylesterase 2b (Ces2b)

Components

Carboxylic ester hydrolase

Keywords

HYDROLASE / carboxylesterase 2b / Ces2b / protein structure / lipid metabolism / X-ray crystallography / alpha/beta-hydrolase fold / biochemistry / lipid hydrolysis / non-alcoholic fatty liver disease

Function / homology

Function and homology information

Aspirin ADME / Phase I - Functionalization of compounds / Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases / hydrolase activity
Similarity search - Function

Biological species

Mus musculus (house mouse)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.55 Å

Authors

Rammer, L. / Eisner, H. / Sagmeister, T. / Oberer, M.

Funding support

Austria, 2items

Citation

Journal: to be published
Title: Crystal structure of mouse Carboxylesterase 2 (Ces2b)
Authors: Rammer, L. / Eisner, H. / Sagmeister, T. / Riegler-Berket, L. / Rodriguez Gamez, C. / Chalhoub, G. / Liesinger, L. / Birner-Gruenberger, R. / Haemmerle, G. / Schoiswohl, G. / Pavkov-Keller, T. / Oberer, M.

History

Deposition	Sep 11, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Sep 24, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9grb.cif.gz	983 KB	Display	PDBx/mmCIF format
PDB format	pdb9grb.ent.gz	694.2 KB	Display	PDB format
PDBx/mmJSON format	9grb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9grb_validation.pdf.gz	942.8 KB	Display	wwPDB validaton report
Full document	9grb_full_validation.pdf.gz	959.3 KB	Display
Data in XML	9grb_validation.xml.gz	88.3 KB	Display
Data in CIF	9grb_validation.cif.gz	116.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/9grb ftp://data.pdbj.org/pub/pdb/validation_reports/gr/9grb	HTTPS FTP

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Related structure data

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
Related items in Molecule of the Month	#240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #54 - Jun 2004 Acetylcholinesterase similarity (6)

Deposited unit

D: Carboxylic ester hydrolase

A: Carboxylic ester hydrolase

B: Carboxylic ester hydrolase

C: Carboxylic ester hydrolase

hetero molecules

234 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

D: Carboxylic ester hydrolase

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

2

A: Carboxylic ester hydrolase

hetero molecules

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

3

B: Carboxylic ester hydrolase

hetero molecules

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

4

C: Carboxylic ester hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	180.75, 109.801, 135.435
Angle α, β, γ (deg.)	90, 92.886, 90
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-820- HOH
2	1	A-873- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	D
2	1	A
3	2	D
4	2	B
5	3	D
6	3	C
7	4	A
8	4	B
9	5	A
10	5	C
11	6	B
12	6	C

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	SER	SER	SER	SER	D	A	29 - 549	1 - 521
2	1	1	SER	SER	SER	SER	A	B	29 - 549	1 - 521
3	2	2	SER	SER	SER	SER	D	A	29 - 549	1 - 521
4	2	2	SER	SER	SER	SER	B	C	29 - 549	1 - 521
5	3	3	PRO	PRO	SER	SER	D	A	30 - 549	2 - 521
6	3	3	PRO	PRO	SER	SER	C	D	30 - 549	2 - 521
7	4	4	SER	SER	SER	SER	A	B	29 - 549	1 - 521
8	4	4	SER	SER	SER	SER	B	C	29 - 549	1 - 521
9	5	5	PRO	PRO	ALA	ALA	A	B	30 - 548	2 - 520
10	5	5	PRO	PRO	ALA	ALA	C	D	30 - 548	2 - 520
11	6	6	PRO	PRO	SER	SER	B	C	30 - 549	2 - 521
12	6	6	PRO	PRO	SER	SER	C	D	30 - 549	2 - 521

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12

#1: Protein

Carboxylic ester hydrolase

Mass: 58166.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mus musculus (house mouse) / Gene: Ces2b, BC015286 / Cell (production host): Expi293F Cells / Production host:

Homo sapiens (human)
References: UniProt: Q6PDB7, Hydrolases; Acting on ester bonds; Carboxylic-ester hydrolases

#2: Polysaccharide

alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2 / Source method: isolated from a natural source

Descriptor	Type	Program
LFucpa1-6DGlcpNAcb1-ROH	Glycam Condensed Sequence	GMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1	WURCS	PDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][b-L-Fucp]{}}	LINUCS	PDB-CARE

#3: Sugar

ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE

Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₈H₁₅NO₆

Identifier	Type	Program
DGlcpNAcb	CONDENSED IUPAC CARBOHYDRATE SYMBOL	GMML 1.0
N-acetyl-b-D-glucopyranosamine	COMMON NAME	GMML 1.0
b-D-GlcpNAc	IUPAC CARBOHYDRATE SYMBOL	PDB-CARE 1.0
GlcNAc	SNFG CARBOHYDRATE SYMBOL	GMML 1.0

#4: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 571 / Source method: isolated from a natural source / Formula: H₂O

Has ligand of interest

N

Has protein modification

Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.67 Å³/Da / Density % sol: 53.94 %
Crystal grow	Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: H2 Morpheus II screen (40 mM polyamines (0.1 M spermine tetrahydrochloride, 0.1 M spermidine trihydrochloride, 0.1 M 1,4-diaminobutane dihydrochloride, 0.1 M DL-ornithine monohydrochloride), ...Details: H2 Morpheus II screen (40 mM polyamines (0.1 M spermine tetrahydrochloride, 0.1 M spermidine trihydrochloride, 0.1 M 1,4-diaminobutane dihydrochloride, 0.1 M DL-ornithine monohydrochloride), 0.1 M buffer system 4 at pH 6.5 (1 M MOPSO, Bis-Tris), and 32.5% v/v precipitant mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-hexanetriol))

Crystal

Density Matthews: 2.67 Å³/Da / Density % sol: 53.94 %

Crystal grow

Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: H2 Morpheus II screen (40 mM polyamines (0.1 M spermine tetrahydrochloride, 0.1 M spermidine trihydrochloride, 0.1 M 1,4-diaminobutane dihydrochloride, 0.1 M DL-ornithine monohydrochloride), ...

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03319 Å
Detector	Type: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 26, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.03319 Å / Relative weight: 1
Reflection	Resolution: 2.55→46.91 Å / Num. obs: 85640 / % possible obs: 99.26 % / Redundancy: 7 % / B_iso Wilson estimate: 60.07 Å² / CC_1/2: 0.998 / CC star: 1 / R_merge(I) obs: 0.08605 / R_pim(I) all: 0.03497 / R_rim(I) all: 0.09302 / Net I/σ(I): 15.26
Reflection shell	Resolution: 2.55→2.641 Å / Redundancy: 7.3 % / R_merge(I) obs: 0.7941 / Mean I/σ(I) obs: 2.66 / Num. unique obs: 8583 / CC_1/2: 0.862 / CC star: 0.962 / R_pim(I) all: 0.316 / R_rim(I) all: 0.8556 / % possible all: 99.93

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0430 (refmacat 0.4.105)	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→46.905 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.947 / SU B: 17.221 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.494 / ESU R Free: 0.243 / Details: Hydrogens have not been used

	R_factor	Num. reflection	% reflection
R_free	0.2049	4466	5.215 %
R_work	0.1709	81166	-
all	0.173	-	-
obs	-	85632	99.277 %

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: 69.146 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.066 Å²	0 Å²	0.021 Å²
2-	-	0.052 Å²	0 Å²
3-	-	-	0.012 Å²

Refinement step

Cycle: LAST / Resolution: 2.55→46.905 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16234	0	62	571	16867

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.012	16746
X-RAY DIFFRACTION	r_angle_refined_deg	1.805	1.811	22762
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.616	5	2073
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	7.086	5	84
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.098	10	2731
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.881	10	738
X-RAY DIFFRACTION	r_chiral_restr	0.125	0.2	2503
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	12902
X-RAY DIFFRACTION	r_nbd_refined	0.215	0.2	7198
X-RAY DIFFRACTION	r_nbtor_refined	0.305	0.2	11450
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	687
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.288	0.2	169
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.182	0.2	26
X-RAY DIFFRACTION	r_mcbond_it	4.016	4.232	8307
X-RAY DIFFRACTION	r_mcangle_it	6.08	7.618	10375
X-RAY DIFFRACTION	r_scbond_it	5.818	4.618	8439
X-RAY DIFFRACTION	r_scangle_it	8.285	8.286	12387
X-RAY DIFFRACTION	r_lrange_it	11.378	53.327	71977
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.098	0.05	16945
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.096	0.05	16960
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.087	0.05	17041
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.08	0.05	17114
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.097	0.05	17034
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.094	0.05	16973

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	D	X-RAY DIFFRACTION	Local ncs	0.09805	0.0501
1	2	A	X-RAY DIFFRACTION	Local ncs	0.09805	0.0501
2	3	D	X-RAY DIFFRACTION	Local ncs	0.09596	0.0501
2	4	B	X-RAY DIFFRACTION	Local ncs	0.09596	0.0501
3	5	D	X-RAY DIFFRACTION	Local ncs	0.08732	0.0501
3	6	C	X-RAY DIFFRACTION	Local ncs	0.08732	0.0501
4	7	A	X-RAY DIFFRACTION	Local ncs	0.08027	0.0501
4	8	B	X-RAY DIFFRACTION	Local ncs	0.08027	0.0501
5	9	A	X-RAY DIFFRACTION	Local ncs	0.09724	0.0501
5	10	C	X-RAY DIFFRACTION	Local ncs	0.09724	0.0501
6	11	B	X-RAY DIFFRACTION	Local ncs	0.09361	0.0501
6	12	C	X-RAY DIFFRACTION	Local ncs	0.09361	0.0501

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
2.55-2.616	0.322	283	0.271	6046	0.273	6334	0.94	0.954	99.9211	0.237
2.616-2.688	0.265	276	0.246	5898	0.247	6180	0.954	0.965	99.9029	0.21
2.688-2.765	0.266	290	0.227	5682	0.229	5985	0.959	0.97	99.7828	0.195
2.765-2.85	0.263	312	0.206	5534	0.209	5856	0.961	0.975	99.8292	0.177
2.85-2.943	0.229	337	0.196	5302	0.198	5660	0.968	0.978	99.629	0.167
2.943-3.046	0.224	323	0.171	5135	0.174	5485	0.968	0.983	99.5078	0.147
3.046-3.16	0.207	261	0.172	4964	0.174	5245	0.973	0.983	99.6187	0.151
3.16-3.289	0.216	272	0.161	4809	0.164	5114	0.971	0.984	99.3547	0.146
3.289-3.434	0.225	244	0.161	4541	0.164	4889	0.97	0.984	97.8728	0.15
3.434-3.601	0.205	253	0.161	4224	0.163	4641	0.977	0.985	96.4663	0.154
3.601-3.795	0.2	246	0.159	4233	0.161	4480	0.979	0.987	99.9777	0.155
3.795-4.023	0.178	231	0.158	3949	0.159	4185	0.984	0.987	99.8805	0.157
4.023-4.299	0.178	241	0.163	3733	0.164	3977	0.983	0.988	99.9246	0.164
4.299-4.64	0.182	218	0.156	3447	0.158	3692	0.983	0.989	99.2687	0.161
4.64-5.078	0.179	168	0.145	3223	0.146	3415	0.981	0.988	99.2972	0.153
5.078-5.669	0.217	156	0.17	2909	0.172	3097	0.97	0.984	98.9667	0.179
5.669-6.53	0.207	113	0.186	2584	0.187	2744	0.976	0.982	98.2872	0.197
6.53-7.959	0.195	116	0.176	2167	0.177	2343	0.978	0.985	97.4392	0.189
7.959-11.097	0.177	86	0.142	1740	0.143	1826	0.984	0.99	100	0.16
11.097-46.905	0.254	40	0.193	1046	0.195	1091	0.95	0.978	99.5417	0.219

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	0.9355	0.1168	0.0005	0.8093	-0.5613	2.8853	-0.0671	-0.011	0.1865	0.0733	-0.1385	-0.2802	-0.1663	0.315	0.2056	0.1023	0.0255	-0.0677	0.1785	0.149	0.278	65.0583	-74.2218	101.7037
2	1.148	0.1864	-0.0958	2.0711	-0.8165	1.3361	0.1319	0.118	0.0416	-0.0381	-0.0455	0.209	0.09	-0.3516	-0.0864	0.0594	-0.0453	-0.013	0.1762	0.0095	0.0252	-24.6103	-54.2987	4.1231
3	2.8379	-0.0839	0.6748	0.6161	0.0413	0.7262	0.049	-0.1906	-0.1791	0.0908	0.0721	-0.0393	0.3391	0.0091	-0.1211	0.4085	-0.085	-0.0622	0.1211	0.035	0.0494	-3.1531	-69.168	40.8764
4	1.8615	0.5295	0.8198	0.8712	-0.154	2.316	-0.1212	0.2808	0.1052	-0.1136	-0.1128	-0.2077	-0.198	0.1224	0.234	0.2167	0.0714	-0.021	0.1179	0.0699	0.141	42.0314	-58.3622	65.6555

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	ALL	D	29 - 551
2	X-RAY DIFFRACTION	2	ALL	A	29 - 549
3	X-RAY DIFFRACTION	3	ALL	B	29 - 549
4	X-RAY DIFFRACTION	4	ALL	C	30 - 549

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