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- PDB-3w9b: Crystal structure of Candida antarctica lipase B with anion-tag -

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Basic information

Entry
Database: PDB / ID: 3w9b
TitleCrystal structure of Candida antarctica lipase B with anion-tag
ComponentsLipase B
KeywordsHYDROLASE / LIPASE (CARBOXYLIC ESTERASE)
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process
Similarity search - Function
: / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Lipase B
Similarity search - Component
Biological speciesCandida antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKim, S.K. / Lee, H.H. / Park, Y.C. / Jeon, S.T. / Son, S.H. / Min, W.K. / Seo, J.H.
CitationJournal: To be Published
Title: Anion tags improve extracellular production of Candida antarctica lipase B in Escherichia coli
Authors: Kim, S.K. / Lee, H.H. / Park, Y.C. / Jeon, S.T. / Son, S.H. / Min, W.K. / Seo, J.H.
History
DepositionApr 2, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipase B
B: Lipase B
C: Lipase B
D: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,5808
Polymers137,0984
Non-polymers1,4824
Water6,557364
1
A: Lipase B
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2904
Polymers68,5492
Non-polymers7412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-32 kcal/mol
Surface area21180 Å2
MethodPISA
2
C: Lipase B
D: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,2904
Polymers68,5492
Non-polymers7412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3950 Å2
ΔGint-32 kcal/mol
Surface area21180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.659, 123.659, 191.852
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein
Lipase B / CALB


Mass: 34274.465 Da / Num. of mol.: 4 / Fragment: UNP residues 26-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida antarctica (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P41365, triacylglycerol lipase
#2: Chemical
ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.18 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1M phosphate-citrate, 40% PEG600, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 36843 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 2.9→2.95 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCA

1tca


Resolution: 2.9→19.8 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.856 / SU B: 31.377 / SU ML: 0.306 / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26546 1834 5 %RANDOM
Rwork0.23204 ---
obs0.2337 34806 99.63 %-
all-36653 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.268 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9292 0 88 364 9744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.029628
X-RAY DIFFRACTIONr_angle_refined_deg1.0571.9813200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36351264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35825.06332
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.418151360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9291532
X-RAY DIFFRACTIONr_chiral_restr0.0580.21532
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0227304
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 117 -
Rwork0.316 2490 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.116-0.10940.11340.35050.15190.543-0.0794-0.0831-0.0417-0.00640.0390.0161-0.1429-0.1640.04040.10110.09440.02270.1398-0.02380.117912.473230.1162-7.878
20.6024-0.03210.22640.06940.05690.2295-0.18220.011-0.0067-0.01830.08510.0083-0.22780.08810.09710.3034-0.0958-0.07780.0907-0.00350.089444.094647.7876-3.9966
30.1674-0.13-0.16020.2608-0.09180.5651-0.031-0.03750.0028-0.1114-0.00510.03860.21640.04060.03610.21030.02910.01030.0307-0.03470.119732.33-4.254-24.116
40.21040.1987-0.16320.3457-0.13120.20070.0178-0.1455-0.0099-0.0944-0.12320.01320.02950.2250.10540.07180.04820.03720.33290.07440.096963.433114.3082-27.9764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 317
2X-RAY DIFFRACTION2B1 - 317
3X-RAY DIFFRACTION3C1 - 317
4X-RAY DIFFRACTION4D1 - 317

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