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- PDB-5ah0: STRUCTURE OF LIPASE 1 FROM PELOSINUS FERMENTANS -

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Basic information

Entry
Database: PDB / ID: 5ah0
TitleSTRUCTURE OF LIPASE 1 FROM PELOSINUS FERMENTANS
ComponentsLIPASE
KeywordsHYDROLASE
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / lipid catabolic process / extracellular region / metal ion binding
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
: / DI(HYDROXYETHYL)ETHER / triacylglycerol lipase / :
Similarity search - Component
Biological speciesPELOSINUS FERMENTANS DSM 17108 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHromic, A. / Gruber, K. / Biundo, A. / Ribitsch, D. / Quartinello, F. / Perz, V. / Arrell, M.S. / Kalman, F. / Guebitz, G.M.
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2016
Title: Characterization of a Poly(Butylene Adipate-Co-Terephthalate)-Hydrolyzing Lipase from Pelosinus Fermentans.
Authors: Biundo, A. / Hromic, A. / Pavkov-Keller, T. / Gruber, K. / Quartinello, F. / Haernvall, K. / Perz, V. / Arrell, M.S. / Zinn, M. / Ribitsch, D. / Guebitz, G.M.
History
DepositionFeb 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 15, 2016Group: Database references
Revision 1.2Dec 6, 2017Group: Refinement description / Category: pdbx_refine_tls_group / Item: _pdbx_refine_tls_group.selection_details
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 / _struct_conn.ptnr2_label_seq_id / _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
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1747
Polymers85,7912
Non-polymers3825
Water55831
1
A: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,0673
Polymers42,8961
Non-polymers1722
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: LIPASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1064
Polymers42,8961
Non-polymers2113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.800, 91.800, 215.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein LIPASE / PFL1


Mass: 42895.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PELOSINUS FERMENTANS DSM 17108 (bacteria)
Plasmid: PET26B(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I8S946, UniProt: A0A0A0YMQ9*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.36 % / Description: NONE
Crystal growDetails: 0.8 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, 0.1 M TRIS, PH 8.5 AND 0.5 % W/V POLYETHYLENE GLYCOL MONOMETHYL ETHER 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97242
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97242 Å / Relative weight: 1
ReflectionResolution: 2.49→60 Å / Num. obs: 33116 / % possible obs: 99.3 % / Observed criterion σ(I): 3.5 / Redundancy: 12.7 % / Biso Wilson estimate: 47.33 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.1
Reflection shellResolution: 2.49→2.64 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.5 / % possible all: 96.3

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KU0

1ku0


Resolution: 2.5→48.202 Å / SU ML: 0.28 / σ(F): 0.01 / Phase error: 29.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2428 1581 5 %
Rwork0.1935 --
obs0.196 31406 95.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→48.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6042 0 17 31 6090
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066224
X-RAY DIFFRACTIONf_angle_d0.9958463
X-RAY DIFFRACTIONf_dihedral_angle_d12.4612179
X-RAY DIFFRACTIONf_chiral_restr0.039916
X-RAY DIFFRACTIONf_plane_restr0.0051075
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4998-2.58050.30791150.26242445X-RAY DIFFRACTION88
2.5805-2.67270.31981460.2622514X-RAY DIFFRACTION91
2.6727-2.77970.30951410.25482599X-RAY DIFFRACTION93
2.7797-2.90620.30981320.25432604X-RAY DIFFRACTION94
2.9062-3.05940.2731340.24142718X-RAY DIFFRACTION96
3.0594-3.25110.28691640.24052709X-RAY DIFFRACTION97
3.2511-3.5020.261540.23332773X-RAY DIFFRACTION98
3.502-3.85430.28471510.20132668X-RAY DIFFRACTION95
3.8543-4.41170.19961390.14962855X-RAY DIFFRACTION99
4.4117-5.5570.17011540.14552881X-RAY DIFFRACTION100
5.557-48.21050.21291510.16473059X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9324-0.13730.60591.47360.62064.69790.0797-0.1093-0.4608-0.1360.08130.10341.12620.1389-0.07480.7335-0.0359-0.02850.18940.00860.456845.6415-20.98690.5804
21.9386-0.29040.18891.09060.33572.53510.01280.07020.45660.4736-0.1119-0.2477-1.12420.14180.05691.1842-0.1414-0.04730.20320.01250.55445.581520.921775.4203
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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