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- PDB-6isp: structure of Candida antarctica Lipase B mutant -

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Basic information

Entry
Database: PDB / ID: 6isp
Titlestructure of Candida antarctica Lipase B mutant
ComponentsLipase B
KeywordsHYDROLASE / calb
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 speciesPseudozyma antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsCen, Y.X. / Zhou, J.H. / Wu, Q.
CitationJournal: Nat Commun / Year: 2019
Title: Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution.
Authors: Cen, Y. / Singh, W. / Arkin, M. / Moody, T.S. / Huang, M. / Zhou, J. / Wu, Q. / Reetz, M.T.
History
DepositionNov 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)143,26517
Polymers133,7034
Non-polymers9,56313
Water22,1221228
1
D: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1503
Polymers33,4261
Non-polymers1,7242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area400 Å2
ΔGint-3 kcal/mol
Surface area12520 Å2
MethodPISA
2
A: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9146
Polymers33,4261
Non-polymers3,4885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area12590 Å2
MethodPISA
3
C: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0124
Polymers33,4261
Non-polymers2,5863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-3 kcal/mol
Surface area13350 Å2
MethodPISA
4
B: Lipase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1904
Polymers33,4261
Non-polymers1,7643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.980, 155.970, 92.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lipase B / CALB


Mass: 33425.672 Da / Num. of mol.: 4 / Mutation: T57A, A89T, W104V, V149G, A281Y, A282Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudozyma antarctica (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P41365, triacylglycerol lipase
#2: Chemical
ChemComp-CPQ / N,N-BIS(3-D-GLUCONAMIDOPROPYL)DEOXYCHOLAMIDE / DEOXY-BIGCHAP


Mass: 862.056 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C42H75N3O15 / Comment: detergent*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1228 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: calcium acetate 0.2 M HEPES 0.1 M pH 7.5 PEG8000 12% Deoxy-BigCHAP 1.4 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→46.265 Å / Num. obs: 106440 / % possible obs: 98.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.132 / Net I/σ(I): 9.4
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.993 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5225 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TCA

1tca


Resolution: 1.88→46.265 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.9
RfactorNum. reflection% reflection
Rfree0.2383 5490 5.16 %
Rwork0.2135 --
obs0.2152 106351 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.88→46.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9317 0 366 1228 10911
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039979
X-RAY DIFFRACTIONf_angle_d0.92413774
X-RAY DIFFRACTIONf_dihedral_angle_d12.8436067
X-RAY DIFFRACTIONf_chiral_restr0.051654
X-RAY DIFFRACTIONf_plane_restr0.0061741
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8801-1.91250.27432800.30064984X-RAY DIFFRACTION94
1.9125-1.94730.31872610.28435083X-RAY DIFFRACTION95
1.9473-1.98470.24422740.26915033X-RAY DIFFRACTION94
1.9847-2.02520.31562740.26835050X-RAY DIFFRACTION94
2.0252-2.06920.28242640.25825061X-RAY DIFFRACTION94
2.0692-2.11730.26982550.25165012X-RAY DIFFRACTION93
2.1173-2.17030.28362660.24084898X-RAY DIFFRACTION91
2.1703-2.22890.25392750.23875115X-RAY DIFFRACTION95
2.2289-2.29450.28342800.23585025X-RAY DIFFRACTION94
2.2945-2.36850.23342900.23185106X-RAY DIFFRACTION94
2.3685-2.4530.29022840.22865039X-RAY DIFFRACTION94
2.453-2.55120.2232520.22615078X-RAY DIFFRACTION95
2.5512-2.66710.25392600.23155070X-RAY DIFFRACTION94
2.6671-2.80760.22952870.21825076X-RAY DIFFRACTION94
2.8076-2.98320.23932970.21785001X-RAY DIFFRACTION93
2.9832-3.21310.23712750.20664831X-RAY DIFFRACTION90
3.2131-3.53570.21172730.18755125X-RAY DIFFRACTION94
3.5357-4.04540.2012830.18085060X-RAY DIFFRACTION94
4.0454-5.08980.21252610.16645146X-RAY DIFFRACTION94
5.0898-25.02130.22732520.19945054X-RAY DIFFRACTION93
Refinement TLS params.Method: refined / Origin x: -8.0068 Å / Origin y: 1.7143 Å / Origin z: 22.8803 Å
111213212223313233
T0.1193 Å2-0.008 Å20.0099 Å2-0.1831 Å2-0.0211 Å2--0.2485 Å2
L0.1488 °2-0.0341 °20.127 °2-0.0837 °2-0.0936 °2--0.3296 °2
S0.0055 Å °0.0297 Å °-0.0255 Å °-0.0043 Å °0.0109 Å °-0.0073 Å °0.0095 Å °-0.0238 Å °-0.0158 Å °
Refinement TLS groupSelection details: all

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