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- PDB-4k6k: Crystal structure of CALB mutant D223G from Candida antarctica -

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Basic information

Entry
Database: PDB / ID: 4k6k
TitleCrystal structure of CALB mutant D223G from Candida antarctica
ComponentsLipase B
KeywordsHYDROLASE / lipase
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
Biological speciesCandida antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAn, J. / Xie, Y. / Feng, Y. / Wu, G.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Enhanced enzyme kinetic stability by increasing rigidity within the active site.
Authors: Xie, Y. / An, J. / Yang, G. / Wu, G. / Zhang, Y. / Cui, L. / Feng, Y.
History
DepositionApr 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1May 7, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,80711
Polymers68,2492
Non-polymers5599
Water4,432246
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-20 kcal/mol
Surface area23100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.708, 87.091, 138.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Lipase B / CALB


Mass: 34124.418 Da / Num. of mol.: 2 / Mutation: D223G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida antarctica (fungus) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta AoDE3Ai / References: UniProt: P41365, triacylglycerol lipase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.07 Å3/Da / Density % sol: 40.56 % / Mosaicity: 0.847 °
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.2M NaAc, 0.1M Tris-Bis pH6.5, vapor diffusion, hanging drop, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorDetector: CCD / Date: Oct 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 71410 / % possible obs: 94.2 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.118 / Χ2: 1.004 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.666.20.45371641.004195.8
1.66-1.726.20.35571131195.4
1.72-1.86.20.28671281.016195.1
1.8-1.96.30.23470950.999194.7
1.9-2.026.40.20269091.003192.1
2.02-2.176.50.17268111.011190.5
2.17-2.396.50.14967811.009189.8
2.39-2.746.20.12372191.003194.7
2.74-3.456.30.10275540.999198.8
3.45-506.20.07476360.996195.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.913 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.674 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 3598 5 %RANDOM
Rwork0.2349 ---
obs0.2364 71355 94.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.82 Å2 / Biso mean: 21.228 Å2 / Biso min: 7.39 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å20 Å2-0 Å2
2--1.82 Å2-0 Å2
3---1.56 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4571 0 36 246 4853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024719
X-RAY DIFFRACTIONr_angle_refined_deg1.1631.9756461
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4385619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69524.938162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.59315674
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7741516
X-RAY DIFFRACTIONr_chiral_restr0.0720.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223568
LS refinement shellResolution: 1.599→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 250 -
Rwork0.299 4664 -
all-4914 -
obs--94.17 %
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)
10.9574-0.1507-0.05560.45310.10630.34270.05220.13240.1401-0.0186-0.0329-0.0359-0.0329-0.0376-0.01930.04910.01970.00660.02380.01890.0233-11.577817.2955-16.5919
22.57450.9886-0.24160.8237-0.24360.4737-0.12010.0511-0.3228-0.10680.0774-0.11590.10510.00650.04280.0762-0.0070.01790.01690.00310.0504-11.589324.0463-52.1194
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 317
2X-RAY DIFFRACTION2B1 - 317

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