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- PDB-1hqd: PSEUDOMONAS CEPACIA LIPASE COMPLEXED WITH TRANSITION STATE ANALOG... -

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Basic information

Entry
Database: PDB / ID: 1hqd
TitlePSEUDOMONAS CEPACIA LIPASE COMPLEXED WITH TRANSITION STATE ANALOGUE OF 1-PHENOXY-2-ACETOXY BUTANE
ComponentsLIPASE
KeywordsHYDROLASE / Pseudomonas cepacia lipase / racemic sec alcohols / transition state (TS) analogue / molecular modelling
Function / homology
Function and homology information


triacylglycerol lipase / triglyceride lipase activity / lipid catabolic process / extracellular region / metal ion binding
Similarity search - Function
Lipases, serine active site. / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-INK / Triacylglycerol lipase
Similarity search - Component
Biological speciesBurkholderia cepacia (bacteria)
MethodX-RAY DIFFRACTION / isomorphous replacement / Resolution: 2.3 Å
AuthorsLuic, M. / Tomic, S. / Lescic, I. / Ljubovic, E. / Sepac, D. / Sunjic, V. / Vitale, L. / Saenger, W. / Kojic-Prodic, B.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Complex of Burkholderia cepacia lipase with transition state analogue of 1-phenoxy-2-acetoxybutane: biocatalytic, structural and modelling study.
Authors: Luic, M. / Tomic, S. / Lescic, I. / Ljubovic, E. / Sepac, D. / Sunjic, V. / Vitale, L. / Saenger, W. / Kojic-Prodic, B.
History
DepositionDec 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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 / struct_ref_seq_dif / struct_site
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_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_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.pdbx_leaving_atom_flag / _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_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4543
Polymers33,1511
Non-polymers3032
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.060, 46.630, 84.300
Angle α, β, γ (deg.)90.00, 120.86, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein LIPASE / / TRIACYLGLYCEROL LIPASE


Mass: 33150.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The enzyme source was a commercial preparation of Pseudomonas cepacia lipase (LPS AW 02513) obtained from Amano Pharmaceuticals, Co., Nagoya, Japan.
Source: (natural) Burkholderia cepacia (bacteria) / References: UniProt: P22088, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-INK / (RP,SP)-O-(2R)-(1-PHENOXYBUT-2-YL)-METHYLPHOSPHONIC ACID CHLORIDE


Mass: 262.670 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16ClO3P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.2745.71
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2781vapor diffusion, hanging drop7.412-45 % (v/v) MPD, 100 mM sodium citrate, 100 mM Hepes , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K
2782vapor diffusion, hanging drop8.615-36 % (v/v) n-propanol, 0.1 M Tris/HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 5 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-36 %(v/v)n-propanol1reservoir
2100 mMTris-HCl1reservoir
312-45 %(v/v)MPD1reservoir
4100 mMsodium citrate1reservoir
5100 mMHEPES1reservoir
612 mg/mlprotein1drop
76.3 mMsodium phosphate1drop
85 mMpiperazine1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1999 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. all: 13473 / Num. obs: 12973 / Biso Wilson estimate: 12.7 Å2 / Rsym value: 0.056
Reflection shellResolution: 2.3→2.38 Å / Mean I/σ(I) obs: 5.9 / Rsym value: 0.056 / % possible all: 91.5
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 96.7 % / Num. measured all: 44574 / Rmerge(I) obs: 0.056

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9refinement
RefinementMethod to determine structure: isomorphous replacement
Starting model: PDB entry code 3LIP

3lip


Resolution: 2.3→10 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 34545891.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Eng & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.203 1320 10.3 %RANDOM
Rwork0.154 ---
obs0.154 12797 96.7 %-
all-12973 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 93.32 Å2 / ksol: 0.491 e/Å3
Displacement parametersBiso mean: 15.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20.22 Å2
2--2.78 Å20 Å2
3----2.85 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 2.3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 16 288 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.691.5
X-RAY DIFFRACTIONc_mcangle_it1.092
X-RAY DIFFRACTIONc_scbond_it1.112
X-RAY DIFFRACTIONc_scangle_it1.522.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.23 231 11.3 %
Rwork0.172 1818 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PROST.PARAMPROTEIN.LINK
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMPROST.TOP
X-RAY DIFFRACTION5CIS_PEPTIDE.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 15.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.68
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.23 / % reflection Rfree: 11.3 % / Rfactor Rwork: 0.172

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