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- PDB-3icw: Structure of a Circular Permutation on Lipase B from Candida Anta... -

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Basic information

Entry
Database: PDB / ID: 3icw
TitleStructure of a Circular Permutation on Lipase B from Candida Antartica with Bound Suicide Inhibitor
ComponentsLipase B
KeywordsHYDROLASE / CIRCULAR PERMUTATION / SUICIDE INHIBITION / Cleavage on pair of basic residues / Disulfide bond / Glycoprotein / Lipid degradation / Zymogen
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
methyl hydrogen (R)-hexylphosphonate / PHOSPHATE ION / Lipase B
Similarity search - Component
Biological speciesCandida antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsHorton, J.R. / Qian, Z. / Jia, D. / Lutz, S.A. / Cheng, X.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural redesign of lipase B from Candida antarctica by circular permutation and incremental truncation.
Authors: Qian, Z. / Horton, J.R. / Cheng, X. / Lutz, S.
History
DepositionJul 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6175
Polymers32,8991
Non-polymers7184
Water6,089338
1
A: Lipase B
hetero molecules

A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,23310
Polymers65,7982
Non-polymers1,4358
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_766-x+2,-x+y+1,-z+5/31
Buried area4920 Å2
ΔGint-36 kcal/mol
Surface area22240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.746, 111.746, 54.806
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-1094-

HOH

21A-1155-

HOH

31A-1184-

HOH

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Components

#1: Protein Lipase B / CALB


Mass: 32899.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida antarctica (fungus) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P41365, triacylglycerol lipase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / CALB / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / References: triacylglycerol lipase
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MHH / methyl hydrogen (R)-hexylphosphonate


Mass: 180.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H17O3P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RECOMBINANT PROTEIN IS A "CIRCULAR PERMUTATION" OF LIPASE B IN WHICH THE C-TERMINAL SEQUENCE ...THE RECOMBINANT PROTEIN IS A "CIRCULAR PERMUTATION" OF LIPASE B IN WHICH THE C-TERMINAL SEQUENCE AAIVAGPKQNCEPDLMPYARPFAVGKRTCSGIVTP HAS BEEN MOVED TO THE N-TERMINUS WITH THE TP REPLACED WITH G. ALA82 AND THR114 REPRESENT VARIATIONS FROM THE PUBLISHED WILD TYPE SEQUENCE AND THEIR ACCURACY WAS CONFIRMED INDEPENDENTLY BY DNA SEQUENCING

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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 Å3/Da / Density % sol: 59.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 3350, 0.2M SODIUM DIHYDROGEN PHOSPHATE, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 20, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.69→27.8 Å / Num. obs: 44608 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 12.8 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 14.4
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 11.5 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
GLRFphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB CODE 1LBT

1lbt


Resolution: 1.69→27.8 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2125 -RANDOM
Rwork0.18 ---
all0.18 ---
obs0.18 42309 95.4 %-
Displacement parametersBiso mean: 31.7 Å2
Baniso -1Baniso -2Baniso -3
1--4.66 Å2-2.08 Å20 Å2
2---4.66 Å20 Å2
3---9.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-27.8 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.69→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2137 0 45 338 2520
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.69→1.75 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.259 199 -
Rwork0.238 --
obs--87.3 %

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