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- PDB-4zv7: Crystal structure of hexagonal form of lipase B from Candida anta... -

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Basic information

Entry
Database: PDB / ID: 4zv7
TitleCrystal structure of hexagonal form of lipase B from Candida antarctica
ComponentsLipase B
KeywordsHYDROLASE / CAL-B / hexagonal form
Function / homologytriacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Lipase B
Function and homology information
Biological speciesCandida antarctica (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsStrzelczyk, P. / Blaszczyk, J. / Bujacz, G.
CitationJournal: Acta Biochim.Pol. / Year: 2016
Title: Crystal and molecular structure of hexagonal form of lipase B from Candida antarctica.
Authors: Strzelczyk, P. / Bujacz, G.D. / Kiebasinski, P. / Baszczyk, J.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Sep 13, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: 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

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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)33,4652
Polymers33,0401
Non-polymers4241
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area350 Å2
ΔGint4 kcal/mol
Surface area12320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.034, 89.034, 137.257
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Lipase B / CALB


Mass: 33040.238 Da / Num. of mol.: 1 / Fragment: UNP residues 26-342
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida antarctica (fungus) / Production host: Aspergillus oryzae (mold) / References: UniProt: P41365, triacylglycerol lipase
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 24% polyethylene glycol 3350, 0.1M citric acid, and 0.1M sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: OXFORD TITAN CCD / Detector: CCD / Date: Mar 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→77.11 Å / Num. obs: 22034 / % possible obs: 98.1 % / Redundancy: 8.8 % / Net I/σ(I): 24.58

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3W9B

3w9b


Resolution: 2→77.11 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.698 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19276 1032 4.7 %RANDOM
Rwork0.14413 ---
obs0.14654 20971 98.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.891 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20.16 Å20 Å2
2--0.32 Å20 Å2
3----1.04 Å2
Refinement stepCycle: 1 / Resolution: 2→77.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 28 332 2684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022449
X-RAY DIFFRACTIONr_bond_other_d0.0020.022289
X-RAY DIFFRACTIONr_angle_refined_deg1.9641.9833371
X-RAY DIFFRACTIONr_angle_other_deg1.13635296
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7445324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75624.70685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02415348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0361510
X-RAY DIFFRACTIONr_chiral_restr0.1190.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212805
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02517
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it11.7431281
X-RAY DIFFRACTIONr_mcbond_other0.991.7411280
X-RAY DIFFRACTIONr_mcangle_it1.5372.6071604
X-RAY DIFFRACTIONr_mcangle_other1.5412.6081605
X-RAY DIFFRACTIONr_scbond_it1.3951.911168
X-RAY DIFFRACTIONr_scbond_other1.3951.9131169
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1322.8171766
X-RAY DIFFRACTIONr_long_range_B_refined5.5116.2033035
X-RAY DIFFRACTIONr_long_range_B_other5.50916.2173036
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 64 -
Rwork0.175 1418 -
obs--91.48 %
Refinement TLS params.Method: refined / Origin x: 25.1757 Å / Origin y: 11.8976 Å / Origin z: 16.3273 Å
111213212223313233
T0.0489 Å20.0084 Å20.0203 Å2-0.0081 Å2-0.0042 Å2--0.0248 Å2
L0.5089 °2-0.0066 °20.2814 °2-0.2068 °2-0.213 °2--0.3678 °2
S-0.0121 Å °-0.0414 Å °0.0386 Å °-0.0734 Å °-0.0298 Å °-0.0256 Å °0.0683 Å °0.0054 Å °0.0419 Å °

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