PDB-9bd4: YjfP, Klebsiella pneumoniae serine hydrolase, unbound

ID or keywords:

Entry

Database: PDB / ID: 9bd4

Title

YjfP, Klebsiella pneumoniae serine hydrolase, unbound

Components

Esterase

Keywords

HYDROLASE / Serine hydrolase / Klebsiella pneumoniae

Function / homology

Function and homology information

acylglycerol lipase / monoacylglycerol lipase activity / carboxylic ester hydrolase activity / serine-type peptidase activity / proteolysis
Similarity search - Function

Biological species

Klebsiella pneumoniae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.3 Å

Authors

Randall, G.T. / Fellner, M.

Funding support

New Zealand, 1items

Citation

Journal: To Be Published
Title: Klebsiella pneumoniae Serine Hydrolase
Authors: Randall, G.T.

History

Deposition	Apr 11, 2024	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 30, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9bd4.cif.gz	206.6 KB	Display	PDBx/mmCIF format
PDB format	pdb9bd4.ent.gz	165.6 KB	Display	PDB format
PDBx/mmJSON format	9bd4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/bd/9bd4 ftp://data.pdbj.org/pub/pdb/validation_reports/bd/9bd4	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	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (2)

Deposited unit

A: Esterase

B: Esterase

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	102.706, 68.195, 65.363
Angle α, β, γ (deg.)	90.00, 77.16, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-437- HOH

#1: Protein	Esterase Mass: 26832.584 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: N-terminal GPG/C-terminal A. Expression / Source: (gene. exp.) Klebsiella pneumoniae (bacteria) Gene: CK244_008325, NCTC13465_04963, NCTC5052_05330, NCTC9601_05351, NCTC9617_04952, NCTC9645_01577, NCTC9661_05640, SAMEA3512100_04172, SAMEA4873632_04766 Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A060VRI4, acylglycerol lipase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 305 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.08 Å³/Da / Density % sol: 40.85 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 0.1 M ammonium sulfate, 35% w/v PEG 8,000, sodium acetate pH 5.0

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2024
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.954 Å / Relative weight: 1
Reflection	Resolution: 1.3→45.11 Å / Num. obs: 106974 / % possible obs: 99.2 % / Redundancy: 4.8 % / CC_1/2: 0.998 / R_merge(I) obs: 0.124 / R_pim(I) all: 0.062 / R_rim(I) all: 0.139 / Χ²: 0.96 / Net I/σ(I): 9.6 / Num. measured all: 513218
Reflection shell	Resolution: 1.3→1.32 Å / % possible obs: 97.4 % / Redundancy: 4.6 % / R_merge(I) obs: 2.794 / Num. measured all: 23779 / Num. unique obs: 5160 / CC_1/2: 0.369 / R_pim(I) all: 1.433 / R_rim(I) all: 3.152 / Χ²: 0.95 / Net I/σ(I) obs: 1.7

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
Aimless	0.7.8	data scaling
XDS		data reduction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.3→45.11 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1748	5335	5 %
R_work	0.1613	-	-
obs	0.162	106730	98.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 1.3→45.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3750	0	0	305	4055

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	4004
X-RAY DIFFRACTION	f_angle_d	0.886	5460
X-RAY DIFFRACTION	f_dihedral_angle_d	5.478	556
X-RAY DIFFRACTION	f_chiral_restr	0.088	580
X-RAY DIFFRACTION	f_plane_restr	0.008	730

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 (%)
1.3-1.31	0.2809	184	0.2657	3254	X-RAY DIFFRACTION	95
1.31-1.33	0.2881	173	0.242	3281	X-RAY DIFFRACTION	97
1.33-1.35	0.2252	168	0.2345	3294	X-RAY DIFFRACTION	97
1.35-1.36	0.2461	198	0.2333	3323	X-RAY DIFFRACTION	97
1.36-1.38	0.2185	145	0.2241	3318	X-RAY DIFFRACTION	98
1.38-1.4	0.2301	164	0.2195	3402	X-RAY DIFFRACTION	98
1.4-1.42	0.2449	173	0.2156	3308	X-RAY DIFFRACTION	98
1.42-1.44	0.2386	186	0.2163	3323	X-RAY DIFFRACTION	99
1.44-1.46	0.2245	179	0.2017	3342	X-RAY DIFFRACTION	98
1.46-1.49	0.1961	186	0.1843	3353	X-RAY DIFFRACTION	98
1.49-1.51	0.18	197	0.1784	3342	X-RAY DIFFRACTION	99
1.51-1.54	0.1887	188	0.1702	3376	X-RAY DIFFRACTION	99
1.54-1.57	0.1787	180	0.1576	3344	X-RAY DIFFRACTION	99
1.57-1.6	0.1646	201	0.1551	3361	X-RAY DIFFRACTION	99
1.6-1.64	0.186	177	0.1577	3372	X-RAY DIFFRACTION	99
1.64-1.68	0.2049	205	0.1642	3376	X-RAY DIFFRACTION	99
1.68-1.72	0.1711	173	0.1537	3409	X-RAY DIFFRACTION	99
1.72-1.76	0.1586	179	0.1517	3387	X-RAY DIFFRACTION	99
1.76-1.82	0.1728	190	0.1488	3394	X-RAY DIFFRACTION	100
1.82-1.87	0.1707	139	0.1515	3410	X-RAY DIFFRACTION	100
1.87-1.94	0.1803	181	0.1475	3411	X-RAY DIFFRACTION	100
1.94-2.02	0.1919	178	0.1524	3414	X-RAY DIFFRACTION	100
2.02-2.11	0.1706	169	0.1469	3426	X-RAY DIFFRACTION	100
2.11-2.22	0.1766	177	0.1532	3410	X-RAY DIFFRACTION	100
2.22-2.36	0.1715	170	0.1545	3461	X-RAY DIFFRACTION	100
2.36-2.54	0.1494	180	0.1554	3434	X-RAY DIFFRACTION	100
2.54-2.8	0.1632	180	0.1609	3439	X-RAY DIFFRACTION	100
2.8-3.21	0.1725	166	0.1596	3434	X-RAY DIFFRACTION	100
3.21-4.04	0.1448	188	0.1474	3459	X-RAY DIFFRACTION	100
4.04-45.11	0.1481	161	0.1431	3538	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	2.8372	2.7088	-1.447	6.147	-2.9147	3.7483	-0.0579	0.0069	-0.1877	-0.2817	-0.089	-0.3408	0.2064	0.2736	0.1473	0.0806	0.0295	0.0303	0.129	-0.0098	0.135	33.0752	-4.5292	-10.3029
2	1.5255	1.2585	0.3546	1.6029	0.2586	1.7121	-0.0013	0.0371	0.0004	-0.015	0.0116	-0.0858	-0.025	0.1243	0.0041	0.0644	0.0206	0.0099	0.0784	0.0037	0.0902	26.3981	-0.1578	-6.6654
3	6.1908	0.1214	0.6034	2.3837	0.3919	6.0997	0.0502	0.3239	-0.5808	-0.1178	0.0075	0.0511	0.4507	-0.1566	-0.0714	0.1286	-0.0043	0.0097	0.0962	-0.0268	0.1621	16.6127	-16.0213	-6.2592
4	5.3318	2.2157	-0.3355	5.012	2.9205	3.0113	-0.0242	-0.0599	-0.1641	0.0059	-0.0411	0.0702	0.0394	-0.0805	0.0406	0.0759	0.0023	0.0115	0.0324	0.0247	0.0759	11.586	-12.8855	1.454
5	6.8862	2.4102	-1.4355	4.4919	-2.1062	2.3274	0.0195	-0.1657	-0.191	0.138	-0.1583	-0.3501	-0.0217	0.295	0.1094	0.0845	0.0167	-0.0279	0.1345	0.0025	0.1043	33.7595	-4.5005	3.5048
6	1.3371	0.4367	0.2654	0.6241	0.0746	0.624	0.0455	-0.0768	-0.0623	0.1038	-0.0372	-0.005	0.0362	-0.0045	-0.0061	0.0947	0.0019	0.0037	0.0916	-0.0035	0.0954	13.5859	-0.4987	6.9301
7	6.8853	2.3998	5.4889	3.5564	4.2839	7.2888	-0.2206	-0.3076	0.4165	-0.0948	-0.0765	0.2295	-0.4001	-0.243	0.2851	0.0979	0.0103	-0.0034	0.1178	-0.012	0.113	7.3957	10.3802	9.677
8	1.6717	0.1173	0.6296	1.0475	0.2148	2.2774	-0.0553	-0.0553	0.1552	0.0138	-0.0184	-0.0146	-0.1316	0.0207	0.0664	0.0734	0.0051	0.0002	0.0465	-0.0036	0.0892	16.6961	11.9745	-1.0527
9	5.1146	-3.4778	0.73	6.2526	-1.432	4.7012	0.0201	0.2499	0.2677	-0.0809	-0.1354	-0.3865	-0.1759	0.3797	0.1298	0.079	-0.0339	-0.0015	0.1759	0.0061	0.1296	31.4219	4.8547	-23.1249
10	2.6532	-0.8125	0.0648	1.9317	0.1835	1.9648	-0.0615	-0.0078	0.0697	-0.0056	0.0732	-0.1007	-0.0348	0.1675	-0.0217	0.0562	-0.016	0.0011	0.0875	0.0014	0.0624	21.7094	5.2261	-23.2919
11	5.8463	-0.3115	-0.376	6.0635	2.1696	2.4075	-0.0888	-0.0882	0.1831	0.0131	-0.0261	0.16	-0.1786	-0.2268	0.088	0.118	0.0085	-0.0376	0.0546	0.0119	0.095	8.4066	16.0461	-26.907
12	5.5972	-2.6246	-0.0178	4.0506	-1.4016	1.4003	0.1011	0.4584	0.1242	-0.2436	-0.2414	-0.2536	-0.02	0.4361	0.1313	0.1597	-0.0426	0.0334	0.2703	0.0116	0.1048	27.1865	5.1098	-36.2489
13	1.7276	-0.2613	0.8072	2.6045	-0.4547	1.6188	-0.0449	0.0839	-0.0047	-0.0755	0.0149	0.0561	0.0479	0.0758	0.0237	0.0875	-0.0055	0.0037	0.0892	-0.0021	0.0888	13.3419	1.763	-32.8695
14	2.7229	-0.9952	-0.8709	5.0353	0.4472	2.1918	0.0026	0.0874	0.3374	-0.3493	-0.0756	0.3689	-0.3756	-0.3864	0.0576	0.1371	0.031	-0.0445	0.1451	-0.0219	0.1779	0.0545	11.1837	-29.1372
15	4.9086	0.5969	1.1454	2.022	2.2538	5.5796	0.0556	0.1104	0.2904	0.1749	-0.1276	0.1713	-0.3187	-0.1774	0.0878	0.1621	-0.0099	0.0041	0.1295	0.0048	0.11	2.7564	9.0051	-39.2209
16	1.8566	-0.4247	-0.2607	1.1521	1.2601	5.3224	0.0422	0.0434	-0.0354	-0.0739	-0.0828	0.1266	0.1058	-0.3197	0.0441	0.1018	-0.0213	0.0002	0.0671	0.0074	0.0986	2.4759	-4.4086	-30.7909
17	1.2675	-0.2584	-0.0916	1.5638	0.403	2.489	-0.0247	0.0165	-0.0599	-0.0212	-0.0132	0.0315	0.2067	-0.0205	0.0374	0.1107	-0.0088	0.0091	0.0616	0.0018	0.0929	10.8265	-8.7084	-25.5336

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 23 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 24 through 61 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 62 through 73 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 74 through 90 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 91 through 109 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 110 through 191 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 192 through 204 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 205 through 240 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 2 through 23 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 24 through 73 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 74 through 90 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 91 through 109 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 110 through 138 )
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 139 through 158 )
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 159 through 170 )
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 171 through 204 )
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 205 through 240 )

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