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- PDB-2veo: X-ray structure of Candida antarctica lipase A in its closed state. -

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Basic information

Entry
Database: PDB / ID: 2veo
TitleX-ray structure of Candida antarctica lipase A in its closed state.
ComponentsLIPASE A
KeywordsHYDROLASE / LIPASE / INTERFACIAL ACTIVATION / SUBSTRATE SPECIFICITY
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region
Similarity search - Function
434 Repressor (Amino-terminal Domain) - #130 / Secretory lipase / Lipase, secreted / 434 Repressor (Amino-terminal Domain) / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URANYL (VI) ION / Lipase A
Similarity search - Component
Biological speciesPSEUDOZYMA ANTARCTICA (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.2 Å
AuthorsEricsson, D.J. / Kasrayan, A. / Johansson, P. / Bergfors, T. / Sandstrom, A.G. / Backvall, J.E. / Mowbray, S.L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: X-Ray Structure of Candida Antarctica Lipase a Shows a Novel Lid Structure and a Likely Mode of Interfacial Activation.
Authors: Ericsson, D.J. / Kasrayan, A. / Johansson, P. / Bergfors, T. / Sandstrom, A.G. / Backvall, J.E. / Mowbray, S.L.
History
DepositionOct 25, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPASE A
B: LIPASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,7708
Polymers94,4042
Non-polymers1,3666
Water8,395466
1
A: LIPASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9364
Polymers47,2021
Non-polymers7343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: LIPASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8344
Polymers47,2021
Non-polymers6323
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)91.539, 91.539, 299.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.7025, -0.7068, 0.0837), (0.7027, -0.7074, -0.0761), (0.113, 0.0053, 0.9936)
Vector: 80.8888, -27.2256, 32.114)

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Components

#1: Protein LIPASE A


Mass: 47201.984 Da / Num. of mol.: 2 / Fragment: RESIDUES 88-528
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOZYMA ANTARCTICA (fungus)
Description: CANDIDA ANTARCTICA RECLASSIFIED AS PSEUDOZYMA APHIDIS IN 2006.
Plasmid: PPICZALPHA-C / Production host: PICHIA PASTORIS (fungus) / Strain (production host): X33 / References: UniProt: W3VKA4, triacylglycerol lipase
#2: Chemical
ChemComp-IUM / URANYL (VI) ION


Mass: 270.028 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2U
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 466 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsURANYL (VI) ION (IUM): URANYL OXYGENS IMPOSSIBLE TO PLACE DUE TO LOW OCCUPANCY.
Sequence detailsPRIMARY AMINO ACID SEQUENCE UNAVAILABLE FROM ANY DATABASE AT TIME OF DEPOSITION.

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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: 3.2 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.4
Details: 2 MICROLITER 10 MILLIGRAM/MILLILITER PROTEIN IN 0.002M TRIS-HCL, PH 8.0 MIXED WITH 1 MICROLITER 0.2M AMMONIUM SULFATE, 0.1M BIS-TRIS, PH 5.5, AND 25% (W/V) PEG 3350.

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 63098 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10.2
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2 / % possible all: 85.3

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Processing

Software
NameVersionClassification
Omodel building
SCALAdata scaling
SHELXDphasing
MLPHAREphasing
SHARPphasing
Ophasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.698 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3194 5.1 %RANDOM
Rwork0.19 ---
obs0.192 59774 96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.07 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6504 0 23 466 6993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226705
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9371.9599176
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6225858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44725.109274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.17615970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2241516
X-RAY DIFFRACTIONr_chiral_restr0.0610.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.025184
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1710.23198
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.24675
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0960.2430
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.245
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2551.54395
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.45726948
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.56432630
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.9534.52228
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.315 194
Rwork0.256 3679

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