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- PDB-4k5q: Crystal structure of CALB mutant DGLM from Candida antarctica -

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Basic information

Entry
Database: PDB / ID: 4k5q
TitleCrystal structure of CALB mutant DGLM from Candida antarctica
ComponentsLipase B
KeywordsHYDROLASE / Candida Antarctica / 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: 1.49 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 16, 2024Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase B


Theoretical massNumber of molelcules
Total (without water)34,0711
Polymers34,0711
Non-polymers00
Water4,810267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.767, 145.966, 86.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-447-

HOH

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Components

#1: Protein Lipase B / CALB


Mass: 34071.383 Da / Num. of mol.: 1 / Mutation: D223G, 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(DE3) / References: UniProt: P41365, triacylglycerol lipase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.12 Å3/Da / Density % sol: 41.91 % / Mosaicity: 0.316 °
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: 1.45→50 Å / Num. obs: 47645 / % possible obs: 91.3 % / Redundancy: 14.4 % / Rmerge(I) obs: 0.073 / Χ2: 0.998 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.45-1.511.70.2759681118.8
1.5-1.5614.50.21551620.9961100
1.56-1.6314.60.16551750.9961100
1.63-1.7214.70.12751310.9991100
1.72-1.8314.70.10351871.0031100
1.83-1.9714.70.084518711100
1.97-2.1714.70.07151861.0011100
2.17-2.4814.60.07252440.997199.9
2.48-3.1214.40.08852500.997199.7
3.12-5012.90.05551550.996194

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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: 1.49→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.264 / SU ML: 0.049 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2164 2410 5.1 %RANDOM
Rwork0.2016 ---
obs0.2024 47610 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 38.47 Å2 / Biso mean: 17.3839 Å2 / Biso min: 10.74 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---1.18 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.49→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 0 267 2585
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.022380
X-RAY DIFFRACTIONr_angle_refined_deg1.0951.9733269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4455316
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5152582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.30515340
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.267158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2380
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221818
LS refinement shellResolution: 1.486→1.525 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 158 -
Rwork0.242 3022 -
all-3180 -
obs--95.24 %

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