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- PDB-2qua: Crystal structure of LipA from Serratia marcescens -

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Basic information

Entry
Database: PDB / ID: 2qua
TitleCrystal structure of LipA from Serratia marcescens
ComponentsExtracellular lipase
KeywordsHYDROLASE / BETA ROLL / ALPHA/BETA HYDROLASE / HELICAL HAIRPIN
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / calcium ion binding
Similarity search - Function
RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / Serralysin-like metalloprotease, C-terminal / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Extracellular lipase
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsMeier, R. / Baumann, U.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: A calcium-gated lid and a large beta-roll sandwich are revealed by the crystal structure of extracellular lipase from Serratia marcescens.
Authors: Meier, R. / Drepper, T. / Svensson, V. / Jaeger, K.E. / Baumann, U.
History
DepositionAug 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3929
Polymers65,0721
Non-polymers3218
Water5,999333
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.070, 115.070, 104.434
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Extracellular lipase


Mass: 65071.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Strain: SM6 / Gene: lipA / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q59933, triacylglycerol lipase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / 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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 281 K / pH: 4.6
Details: 26% MPD, 0.1 M Na-Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 281K, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.000, 0.780
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 14, 2006
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.781
ReflectionResolution: 1.95→50 Å / Num. obs: 51634 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 4.88 % / Rmerge(I) obs: 0.093 / Rsym value: 0.093 / Net I/σ(I): 12.8
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 4.23 % / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.73 / % possible all: 73

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Processing

Software
NameVersionClassification
REFMAC5.3.0036refinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→46.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.499 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.128 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1195 2.2 %RANDOM
Rwork0.172 ---
obs0.173 51167 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0.72 Å20 Å2
2---1.45 Å20 Å2
3---2.17 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4601 0 8 333 4942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214751
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9356389
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4835614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27925.333225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96315687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4781514
X-RAY DIFFRACTIONr_chiral_restr0.060.2697
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.023694
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.22055
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23209
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2385
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1270.235
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.246
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8421.53122
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.55824759
X-RAY DIFFRACTIONr_scbond_it4.36831854
X-RAY DIFFRACTIONr_scangle_it5.9334.51630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 72 -
Rwork0.291 3081 -
obs--100 %
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)
11.4055-0.1628-0.76193.1187-0.16731.2502-0.0692-0.1537-0.3030.59820.01040.58980.11340.1050.0588-0.0067-0.02820.141-0.08160.00780.047728.3377-2.513523.8956
20.9499-0.2055-0.01053.24150.55380.5398-0.0709-0.0129-0.17450.0504-0.04430.3547-0.0780.01190.1152-0.0875-0.02250.0787-0.1062-0.0165-0.115327.548724.61817.1063
33.9273-0.3396-1.99642.60510.81183.58040.0153-0.22620.2930.3345-0.02290.1-0.1734-0.01030.00750.076-0.00130.0188-0.0469-0.0532-0.173925.3444.814436.3818
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 249
2X-RAY DIFFRACTION2A250 - 461
3X-RAY DIFFRACTION3A462 - 613

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