PDB-7wol: Crystal structure of lipase TrLipB from Thermomocrobium roseum

ID or keywords:

Entry

Database: PDB / ID: 7wol

Title

Crystal structure of lipase TrLipB from Thermomocrobium roseum

Components

Lipase

Keywords

HYDROLASE / Lipid degradation / Lipid metabolism

Function / homology

lipase activity / : / Alpha/beta hydrolase fold-3 / alpha/beta hydrolase fold / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / SUCCINIC ACID / Lipase

Function and homology information

Biological species

Thermomicrobium roseum DSM 5159 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Zhang, L. / Fang, Y. / Shi, Y. / Gu, Z. / Xin, Y.

Funding support

China, 2items

Citation

Journal: To Be Published
Title: Crystal structure of lipase TrLipB from Thermomocrobium roseum
Authors: Fang, Y. / Xin, Y. / Shi, Y. / Gu, Z. / Zhang, L.

History

Deposition	Jan 21, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jan 25, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7wol.cif.gz	151 KB	Display	PDBx/mmCIF format
PDB format	pdb7wol.ent.gz	113.1 KB	Display	PDB format
PDBx/mmJSON format	7wol.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7wol_validation.pdf.gz	487.4 KB	Display	wwPDB validaton report
Full document	7wol_full_validation.pdf.gz	495.2 KB	Display
Data in XML	7wol_validation.xml.gz	29.8 KB	Display
Data in CIF	7wol_validation.cif.gz	43.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wo/7wol ftp://data.pdbj.org/pub/pdb/validation_reports/wo/7wol	HTTPS FTP

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Related structure data

Related structure data	1lzkS S: Starting model for refinement
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

Deposited unit

A: Lipase

B: Lipase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	129.402, 129.402, 122.792
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

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Protein , 1 types, 2 molecules AB

#1: Protein	Lipase Mass: 36696.801 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermomicrobium roseum DSM 5159 (bacteria) Strain: ATCC 27502 / DSM 5159 / P-2 / Gene: trd_1687 / Production host: Bacillus subtilis (bacteria) / References: UniProt: B9L0X7

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Non-polymers , 5 types, 437 molecules

#2: Chemical	ChemComp-SIN / SUCCINIC ACID Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄H₆O₄
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 417 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 3.5 Å³/Da / Density % sol: 64.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1M Succinic acid,0.1M HEPES,7,1% w/vPEG 2000 MME

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 19, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2→45.75 Å / Num. obs: 70819 / % possible obs: 100 % / Redundancy: 14.4 % / R_merge(I) obs: 0.082 / Net I/σ(I): 22.8
Reflection shell	Resolution: 2→2.04 Å / R_merge(I) obs: 0.821 / Num. unique obs: 4504

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0267	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1lzk

1lzk

Resolution: 2→45.75 Å / Cor.coef. F_o:F_c: 0.973 / Cor.coef. F_o:F_c free: 0.962 / SU B: 2.894 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.112 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.1862	3497	4.943 %
R_work	0.1572	67247	-
all	0.159	-	-
obs	-	70744	99.983 %

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: 39.58 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.717 Å²	0 Å²	0 Å²
2-	-	-1.717 Å²	0 Å²
3-	-	-	3.433 Å²

Refinement step

Cycle: LAST / Resolution: 2→45.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4948	0	110	417	5475

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	5190
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.015	5005
X-RAY DIFFRACTION	r_angle_refined_deg	1.454	1.649	7055
X-RAY DIFFRACTION	r_angle_other_deg	1.319	1.57	11461
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.212	5	641
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	27.203	19.799	298
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.394	15	768
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.61	15	61
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	639
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	5840
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1218
X-RAY DIFFRACTION	r_nbd_refined	0.209	0.2	1047
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.183	0.2	4752
X-RAY DIFFRACTION	r_nbtor_refined	0.161	0.2	2484
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.079	0.2	2368
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.161	0.2	379
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.026	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.225	0.2	11
X-RAY DIFFRACTION	r_nbd_other	0.259	0.2	46
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.191	0.2	16
X-RAY DIFFRACTION	r_mcbond_it	2.593	3.838	2555
X-RAY DIFFRACTION	r_mcbond_other	2.592	3.836	2554
X-RAY DIFFRACTION	r_mcangle_it	3.596	5.741	3190
X-RAY DIFFRACTION	r_mcangle_other	3.596	5.743	3191
X-RAY DIFFRACTION	r_scbond_it	3.562	4.356	2635
X-RAY DIFFRACTION	r_scbond_other	3.561	4.357	2636
X-RAY DIFFRACTION	r_scangle_it	5.397	6.329	3862
X-RAY DIFFRACTION	r_scangle_other	5.396	6.331	3863
X-RAY DIFFRACTION	r_lrange_it	7.089	46.555	5806
X-RAY DIFFRACTION	r_lrange_other	7	46.074	5697

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 (%)
2-2.052	0.231	270	0.23	4911	X-RAY DIFFRACTION	99.9807
2.052-2.108	0.252	243	0.21	4774	X-RAY DIFFRACTION	99.9801
2.108-2.169	0.216	232	0.187	4660	X-RAY DIFFRACTION	100
2.169-2.236	0.198	199	0.178	4555	X-RAY DIFFRACTION	100
2.236-2.309	0.184	191	0.163	4409	X-RAY DIFFRACTION	100
2.309-2.39	0.209	213	0.154	4242	X-RAY DIFFRACTION	99.9776
2.39-2.48	0.19	220	0.156	4117	X-RAY DIFFRACTION	100
2.48-2.582	0.191	220	0.165	3940	X-RAY DIFFRACTION	100
2.582-2.696	0.176	233	0.155	3774	X-RAY DIFFRACTION	100
2.696-2.828	0.202	205	0.16	3613	X-RAY DIFFRACTION	100
2.828-2.981	0.192	176	0.16	3477	X-RAY DIFFRACTION	100
2.981-3.161	0.227	163	0.162	3306	X-RAY DIFFRACTION	100
3.161-3.379	0.204	166	0.171	3087	X-RAY DIFFRACTION	100
3.379-3.649	0.18	131	0.155	2930	X-RAY DIFFRACTION	100
3.649-3.997	0.159	166	0.145	2648	X-RAY DIFFRACTION	100
3.997-4.468	0.163	142	0.129	2425	X-RAY DIFFRACTION	100
4.468-5.157	0.151	122	0.123	2154	X-RAY DIFFRACTION	100
5.157-6.311	0.207	82	0.166	1872	X-RAY DIFFRACTION	100
6.311-8.904	0.183	70	0.147	1482	X-RAY DIFFRACTION	100
8.904-45.75	0.166	53	0.173	871	X-RAY DIFFRACTION	99.0354

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