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- PDB-3guu: X-ray structure of Candida Antarctica lipase A -

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Basic information

Entry
Database: PDB / ID: 3guu
TitleX-ray structure of Candida Antarctica lipase A
ComponentsLipase A
KeywordsHYDROLASE / Candida / Lipase / Protein structure
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
Biological speciesCandida Antarctica (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrandt, A.-M. / Li, X.-G. / Nymalm-Rejstrom, Y. / Airenne, T. / Kanerva, L.T. / Salminen, T.A.
CitationJournal: To be Published
Title: The crystal structure of Lipase A from Candida antarctica
Authors: Brandt, A.-M. / Li, X.-G. / Nymalm-Rejstrom, Y. / Airenne, T. / Kanerva, L.T. / Salminen, T.A.
History
DepositionMar 30, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / struct_ref_seq / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)99,3566
Polymers98,6912
Non-polymers6654
Water8,989499
1
A: Lipase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6763
Polymers49,3461
Non-polymers3302
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lipase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6803
Polymers49,3461
Non-polymers3342
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.100, 92.100, 300.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 5 / Auth seq-ID: 12 - 441 / Label seq-ID: 33 - 462

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Lipase A


Mass: 49345.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: Commerial enzyme Roche Chirazyme L-5 / Source: (natural) Candida Antarctica (fungus) / References: UniProt: W3VKA4*PLUS, triacylglycerol lipase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THIS ...THERE IS NO UNP REFERENCE SEQUENCE DATABASE FOR THIS PROTEIN AT THE TIME OF PROCESSING. THIS SEQUENCE IS REFERRED IN CAN.J.BOT. VOL 73 (1995), PP. S869-S875; HOEGH, S. ET.

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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: 3.23 Å3/Da / Density % sol: 61.89 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M Ammonium sulfate, 12% glycerol, 100mM TRIS-HCl pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 88351 / Num. obs: 86764 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.174 / Net I/σ(I): 9.64
Reflection shellResolution: 2.1→2.3 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.433 / Mean I/σ(I) obs: 4.42 / Num. unique all: 17290 / Rsym value: 0.434 / % possible all: 96.4

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Processing

Software
NameVersionClassification
XDSdata scaling
PHASERphasing
REFMAC5.3.0040refinement
INTEGRATEdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEO

2veo


Resolution: 2.1→19.92 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.892 / SU B: 4.309 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23365 3784 5 %RANDOM
Rwork0.18914 ---
obs0.19136 71879 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.292 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6535 0 43 499 7077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0226789
X-RAY DIFFRACTIONr_bond_other_d0.120.028
X-RAY DIFFRACTIONr_angle_refined_deg1.7131.9639286
X-RAY DIFFRACTIONr_angle_other_deg3.689316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1315868
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1925.018277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.09215978
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4551518
X-RAY DIFFRACTIONr_chiral_restr0.1250.21035
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025250
X-RAY DIFFRACTIONr_nbd_refined0.220.23377
X-RAY DIFFRACTIONr_nbd_other0.3750.217
X-RAY DIFFRACTIONr_nbtor_refined0.310.24686
X-RAY DIFFRACTIONr_nbtor_other0.1240.25
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2541
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.210
X-RAY DIFFRACTIONr_mcbond_it0.8691.54444
X-RAY DIFFRACTIONr_mcangle_it1.33927018
X-RAY DIFFRACTIONr_scbond_it2.36632689
X-RAY DIFFRACTIONr_scangle_it3.4874.52268
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1711medium positional0.150.5
1524loose positional0.335
1711medium thermal0.842
1524loose thermal1.1610
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 275 -
Rwork0.204 5208 -
obs-5208 100 %

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