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- PDB-4k6h: Crystal structure of CALB mutant L278M from Candida antarctica -

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Basic information

Entry
Database: PDB / ID: 4k6h
TitleCrystal structure of CALB mutant L278M 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 15, 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 1.3Oct 30, 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)68,8359
Polymers68,4012
Non-polymers4347
Water5,747319
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint2 kcal/mol
Surface area23560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.710, 81.283, 71.556
Angle α, β, γ (deg.)90.000, 95.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lipase B / CALB


Mass: 34200.496 Da / Num. of mol.: 2 / Mutation: L278M
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.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.02 Å3/Da / Density % sol: 39.05 % / Mosaicity: 0.482 °
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: 70860 / % possible obs: 99.3 % / Redundancy: 6 % / Rmerge(I) obs: 0.084 / Χ2: 1.001 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.666.10.34671001.0081100
1.66-1.726.10.28370940.9971100
1.72-1.86.10.21271221.0071100
1.8-1.96.10.16771171.0021100
1.9-2.025.80.14470880.996199.9
2.02-2.1760.09471361.0041100
2.17-2.395.70.08469480.999197.4
2.39-2.746.10.0771380.9931100
2.74-3.456.10.08171581.001199.9
3.45-505.70.05769591.007195.7

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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: 0.947 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 1.597 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 3585 5.1 %RANDOM
Rwork0.1969 ---
obs0.198 70785 98.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 39.63 Å2 / Biso mean: 15.4387 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.82 Å2-0 Å2-0.01 Å2
2--0.73 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4676 0 27 319 5022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.024822
X-RAY DIFFRACTIONr_angle_refined_deg1.1341.9756611
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4935637
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65925.06166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53615686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3851516
X-RAY DIFFRACTIONr_chiral_restr0.0710.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0223664
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.229 249 -
Rwork0.2 4720 -
all-4969 -
obs--96 %

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