PDB-8xy5: Open conformation of Burkholderia stagnalis lipase

ID or keywords:

Entry

Database: PDB / ID: 8xy5

Title

Open conformation of Burkholderia stagnalis lipase

Components

Alpha/beta hydrolase

Keywords

HYDROLASE / triacylglycerol lipase / Burkholderia

Function / homology

alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold / hydrolase activity / Alpha/beta hydrolase

Function and homology information

Biological species

Burkholderia stagnalis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.399 Å

Authors

Kataoka, S. / Kubota, T. / Ishikawa, K.

Funding support

Japan, 1items

Citation

Journal: To Be Published
Title: Structural and functional studies of lipase from Burkholderia stagnalis
Authors: Kataoka, S. / Kubota, T. / Ishikawa, K.

History

Deposition	Jan 19, 2024	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 22, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8xy5.cif.gz	147 KB	Display	PDBx/mmCIF format
PDB format	pdb8xy5.ent.gz	109.1 KB	Display	PDB format
PDBx/mmJSON format	8xy5.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/xy/8xy5 ftp://data.pdbj.org/pub/pdb/validation_reports/xy/8xy5	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	#165 - Sep 2013 Designed Protein Cages similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (1) #220 - Apr 2018 Dehalogenases similarity (2)

Deposited unit

A: Alpha/beta hydrolase

B: Alpha/beta hydrolase

hetero molecules

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

1

A: Alpha/beta hydrolase

hetero molecules

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

2

B: Alpha/beta hydrolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	160.643, 69.210, 51.322
Angle α, β, γ (deg.)	90.000, 98.531, 90.000
Int Tables number	5
Space group name H-M	C121

#1: Protein	Alpha/beta hydrolase / Triacylglycerol lipase Mass: 37472.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Burkholderia stagnalis (bacteria) / Strain: PL266-QLM / References: UniProt: A0A108C1V7
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 601 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y
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: 1.88 Å³/Da / Density % sol: 34.66 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 7 Details: 0.1 M HEPES, pH 7.0, 45% MPD, 1 M ammonium fluoride, 3% methanol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
Detector	Type: ADSC QUANTUM 270 / Detector: CCD / Date: Feb 22, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.399→50 Å / Num. obs: 109236 / % possible obs: 99.8 % / Redundancy: 3.6 % / CC_1/2: 0.996 / Net I/σ(I): 24.5
Reflection shell	Resolution: 1.399→1.42 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.835 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 5480 / CC_1/2: 0.627 / % possible all: 99.9

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.399→29.243 Å / Cor.coef. F_o:F_c: 0.975 / Cor.coef. F_o:F_c free: 0.968 / SU B: 1.02 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.059 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1838	5565	5.095 %
R_work	0.162	103650	-
all	0.163	-	-
obs	0.163	109215	99.666 %

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: 14.617 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.001 Å²	-0 Å²	0 Å²
2-	-	0.001 Å²	-0 Å²
3-	-	-	-0.002 Å²

Refinement step

Cycle: LAST / Resolution: 1.399→29.243 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4682	0	39	601	5322

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.003	0.012	4840
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	4526
X-RAY DIFFRACTION	r_angle_refined_deg	1.19	1.784	6634
X-RAY DIFFRACTION	r_angle_other_deg	0.441	1.715	10350
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.122	5	646
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	4.802	5	22
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	9.793	10	690
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	14.559	10	200
X-RAY DIFFRACTION	r_chiral_restr	0.062	0.2	789
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5856
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1112
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1020
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.196	0.2	4090
X-RAY DIFFRACTION	r_nbtor_refined	0.173	0.2	2529
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	2329
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.108	0.2	432
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.006	0.2	1
X-RAY DIFFRACTION	r_metal_ion_refined	0.076	0.2	11
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.171	0.2	21
X-RAY DIFFRACTION	r_nbd_other	0.228	0.2	112
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.155	0.2	36
X-RAY DIFFRACTION	r_mcbond_it	0.642	1.475	2562
X-RAY DIFFRACTION	r_mcbond_other	0.642	1.475	2562
X-RAY DIFFRACTION	r_mcangle_it	1.015	2.654	3202
X-RAY DIFFRACTION	r_mcangle_other	1.015	2.654	3203
X-RAY DIFFRACTION	r_scbond_it	1.12	1.632	2278
X-RAY DIFFRACTION	r_scbond_other	1.119	1.633	2279
X-RAY DIFFRACTION	r_scangle_it	1.795	2.951	3426
X-RAY DIFFRACTION	r_scangle_other	1.795	2.951	3427
X-RAY DIFFRACTION	r_lrange_it	3.474	17.27	5715
X-RAY DIFFRACTION	r_lrange_other	3.075	15.683	5540

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
1.399-1.435	0.301	440	0.288	7614	0.288	8111	0.933	0.938	99.2972	0.288
1.435-1.475	0.278	438	0.266	7417	0.266	7856	0.938	0.947	99.9873	0.266
1.475-1.517	0.246	362	0.237	7213	0.237	7577	0.958	0.961	99.9736	0.237
1.517-1.564	0.224	369	0.211	7091	0.212	7460	0.964	0.97	100	0.211
1.564-1.615	0.206	357	0.196	6803	0.196	7164	0.972	0.975	99.9442	0.196
1.615-1.672	0.219	353	0.188	6615	0.19	6972	0.97	0.978	99.9426	0.188
1.672-1.734	0.216	322	0.174	6374	0.176	6702	0.973	0.982	99.9105	0.174
1.734-1.805	0.212	334	0.168	6096	0.17	6436	0.973	0.983	99.9068	0.168
1.805-1.885	0.191	319	0.17	5913	0.171	6236	0.98	0.983	99.9359	0.17
1.885-1.976	0.177	286	0.151	5649	0.152	5949	0.982	0.987	99.7647	0.151
1.976-2.083	0.156	307	0.139	5339	0.14	5653	0.986	0.989	99.8762	0.139
2.083-2.208	0.147	266	0.135	5076	0.135	5347	0.987	0.989	99.9065	0.135
2.208-2.36	0.169	246	0.135	4771	0.137	5021	0.983	0.989	99.9203	0.135
2.36-2.548	0.159	249	0.131	4442	0.133	4696	0.985	0.99	99.8935	0.131
2.548-2.789	0.148	219	0.132	4118	0.133	4338	0.986	0.99	99.9769	0.132
2.789-3.114	0.173	197	0.14	3715	0.142	3912	0.983	0.989	100	0.14
3.114-3.589	0.144	190	0.138	3290	0.139	3484	0.988	0.989	99.8852	0.138
3.589-4.38	0.192	137	0.148	2777	0.15	2958	0.979	0.987	98.5125	0.148
4.38-6.125	0.188	103	0.183	2152	0.183	2301	0.982	0.981	98.0009	0.183
6.125-29.243	0.234	71	0.226	1185	0.227	1370	0.979	0.974	91.6788	0.226

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