PDB-9fde: Lipase calB candida antarctica with lysine ligand

ID or keywords:

Entry

Database: PDB / ID: 9fde

Title

Lipase calB candida antarctica with lysine ligand

Components

(Lipase B) x 2

Keywords

HYDROLASE / lipase

Function / homology

: / triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold / LYSINE / Lipase B

Function and homology information

Biological species

Moesziomyces antarcticus (fungus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.999 Å

Authors

Jelsch, C. / Favier, F. / Didierjean, C.

Funding support

France, 1items

Citation

Journal: To Be Published
Title: Lipase calB candida antarctica with lysine ligand
Authors: Jelsch, C. / Favier, F. / Didierjean, C.

History

Deposition	May 16, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 28, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9fde.cif.gz	132.9 KB	Display	PDBx/mmCIF format
PDB format	pdb9fde.ent.gz	97.8 KB	Display	PDB format
PDBx/mmJSON format	9fde.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/fd/9fde ftp://data.pdbj.org/pub/pdb/validation_reports/fd/9fde	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

Deposited unit

A: Lipase B

B: Lipase B

hetero molecules

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

1

A: Lipase B

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

2

B: Lipase B

hetero molecules

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

Unit cell

Length a, b, c (Å)	45.318, 107.476, 68.235
Angle α, β, γ (deg.)	90.000, 90.043, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Lipase B / CALB Mass: 33040.238 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moesziomyces antarcticus (fungus) / Production host: Escherichia coli B (bacteria) / References: UniProt: P41365, triacylglycerol lipase
#2: Protein	Lipase B / CALB Mass: 32842.023 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Moesziomyces antarcticus (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P41365, triacylglycerol lipase
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-LYS / LYSINE Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₅N₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.52 Å³/Da / Density % sol: 51.23 % / Description: Platelet-shaped
Crystal grow	Temperature: 293 K / Method: vapor diffusion Details: Propan-2-ol 40 % (V/V), PEG 8000 18 % (W/V), 100mM Imidazole/HCl pH 6.2

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.980121 Å

Detector

Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 20, 2020

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.980121 Å / Relative weight: 1

Reflection twin

Type	Crystal-ID	ID	Operator	Domain-ID	Fraction
pseudo-merohedral	1	1	H, K, L	1	0.4317
pseudo-merohedral	2	2	-h,-k,l	2	0.5683

Reflection

Resolution: 1.87→45.32 Å / Num. obs: 52748 / % possible obs: 98 % / Redundancy: 6.7 % / CC_1/2: 0.995 / R_merge(I) obs: 0.146 / Net I/σ(I): 8.5

Reflection shell

Resolution: 1.87→1.91 Å / Num. unique obs: 2665 / CC_1/2: 0.672

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
XDS		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.999→45.318 Å / Cor.coef. F_o:F_c: 0.937 / Cor.coef. F_o:F_c free: 0.89 / WR_factor R_free: 0.229 / WR_factor R_work: 0.179 / SU B: 4.023 / SU ML: 0.116 / Average fsc free: 0.9493 / Average fsc work: 0.968 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2571	2058	4.691 %
R_work	0.2049	41809	-
all	0.207	-	-
obs	-	43867	99.289 %

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: 21.891 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.219 Å²	0 Å²	3.471 Å²
2-	-	-16.929 Å²	-0 Å²
3-	-	-	23.149 Å²

Refinement step

Cycle: LAST / Resolution: 1.999→45.318 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4633	0	11	129	4773

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.01	0.013	4799
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4362
X-RAY DIFFRACTION	r_angle_refined_deg	1.81	1.645	6600
X-RAY DIFFRACTION	r_angle_other_deg	1.344	1.561	10192
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.845	5	640
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.181	23.736	182
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.469	15	690
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.432	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.081	0.2	661
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.02	5441
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	895
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1180
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.199	0.2	4456
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	2422
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.087	0.2	1965
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.205	0.2	234
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.125	0.2	3
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.237	0.2	15
X-RAY DIFFRACTION	r_nbd_other	0.217	0.2	52
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.216	0.2	11
X-RAY DIFFRACTION	r_mcbond_it	1.769	2.356	2551
X-RAY DIFFRACTION	r_mcbond_other	1.766	2.356	2550
X-RAY DIFFRACTION	r_mcangle_it	2.262	3.53	3191
X-RAY DIFFRACTION	r_mcangle_other	2.262	3.531	3192
X-RAY DIFFRACTION	r_scbond_it	1.659	2.397	2248
X-RAY DIFFRACTION	r_scbond_other	1.659	2.397	2248
X-RAY DIFFRACTION	r_scangle_it	2.18	3.574	3408
X-RAY DIFFRACTION	r_scangle_other	2.178	3.574	3408
X-RAY DIFFRACTION	r_lrange_it	2.991	28.965	5495
X-RAY DIFFRACTION	r_lrange_other	2.982	28.961	5489

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 (%)
1.999-2.051	0.338	139	0.244	3008	X-RAY DIFFRACTION	96.5337
2.051-2.107	0.317	159	0.225	2977	X-RAY DIFFRACTION	99.3034
2.107-2.168	0.286	116	0.221	2954	X-RAY DIFFRACTION	99.3849
2.168-2.235	0.464	134	0.509	2834	X-RAY DIFFRACTION	99.1647
2.235-2.308	0.609	163	0.538	2698	X-RAY DIFFRACTION	98.9965
2.308-2.389	0.239	116	0.192	2717	X-RAY DIFFRACTION	99.4035
2.389-2.479	0.238	122	0.18	2568	X-RAY DIFFRACTION	99.2986
2.479-2.58	0.239	130	0.195	2453	X-RAY DIFFRACTION	99.9613
2.58-2.694	0.272	105	0.177	2398	X-RAY DIFFRACTION	99.3254
2.694-2.826	0.253	127	0.195	2313	X-RAY DIFFRACTION	99.9181
2.826-2.978	0.242	135	0.197	2085	X-RAY DIFFRACTION	99.507
2.978-3.158	0.262	105	0.195	2070	X-RAY DIFFRACTION	100.1381
3.158-3.376	0.232	113	0.191	1899	X-RAY DIFFRACTION	99.5054
3.376-3.646	0.206	77	0.195	1807	X-RAY DIFFRACTION	99.7353
3.646-3.993	0.225	89	0.182	1656	X-RAY DIFFRACTION	99.8855
3.993-4.462	0.17	70	0.138	1512	X-RAY DIFFRACTION	99.8107
4.462-5.149	0.166	64	0.126	1334	X-RAY DIFFRACTION	99.5018
5.149-6.297	0.222	30	0.155	1145	X-RAY DIFFRACTION	99.4078
6.297-8.867	0.138	34	0.128	890	X-RAY DIFFRACTION	99.784
8.867-45.3	0.19	30	0.141	491	X-RAY DIFFRACTION	98.8615

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