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- PDB-2qub: Crystal structure of extracellular lipase LipA from Serratia marc... -

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Basic information

Entry
Database: PDB / ID: 2qub
TitleCrystal structure of extracellular lipase 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 / 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 / _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
C: Extracellular lipase
E: Extracellular lipase
G: Extracellular lipase
I: Extracellular lipase
K: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)392,35554
Polymers390,4316
Non-polymers1,92448
Water34,6071921
1
A: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3929
Polymers65,0721
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3929
Polymers65,0721
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3929
Polymers65,0721
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3929
Polymers65,0721
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3929
Polymers65,0721
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Extracellular lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3929
Polymers65,0721
Non-polymers3218
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.401, 202.401, 317.731
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Extracellular lipase


Mass: 65071.801 Da / Num. of mol.: 6
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.: 48 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1921 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 281 K / pH: 4.6
Details: 26% MPD, 0.1M 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: X06SA / Wavelength: 0.987
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2007
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 430068 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 24 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.335 / % possible all: 76.7

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Processing

Software
NameVersionClassification
REFMAC5.3.0036refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→24.93 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.77 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1275 30 %RANDOM
Rwork0.171 ---
obs0.171 428693 95.6 %-
all-430068 --
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: 23.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27606 0 48 1921 29575
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02128510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0981.93538334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.14953684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22425.3331350
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.553154122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5641584
X-RAY DIFFRACTIONr_chiral_restr0.0610.24182
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0222164
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2150.210765
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3140.218941
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.21681
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0690.2186
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.2192
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.218
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5431.518834
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.031228554
X-RAY DIFFRACTIONr_scbond_it3.258311123
X-RAY DIFFRACTIONr_scangle_it4.6934.59780
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 69 -
Rwork0.228 24684 -
obs--74.01 %
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)
11.3478-0.1447-0.17491.41810.78641.2978-0.0377-0.19960.02750.1132-0.02190.26140.0522-0.16080.0596-0.10550.02390.0222-0.0628-0.0017-0.0534-70.2396-29.862923.1603
22.008-0.48590.32640.71740.0810.5381-0.04460.0285-0.00280.0020.0197-0.0105-0.02710.08420.0249-0.10290.00180.0062-0.1127-0.01-0.1272-41.8731-28.551817.4648
32.3277-0.19960.54392.68070.82882.6446-0.171-0.31840.14160.13190.1368-0.1802-0.16010.08420.0341-0.06010.039-0.04570.0449-0.0278-0.0842-21.971-26.041437.3747
41.04010.0864-0.4071.3771-0.40171.1322-0.0426-0.1196-0.14010.16260.0304-0.10680.05850.15310.0123-0.08070.0208-0.0181-0.1023-0.0051-0.0983-40.362410.901524.93
50.5938-0.4194-0.05911.69040.07290.3256-0.00820.01880.0347-0.0289-0.0106-0.0015-0.0375-0.01710.0187-0.1085-0.00240.0064-0.11810.0027-0.1312-55.99334.485918.7758
61.5223-0.0567-0.81931.5291-0.34872.9197-0.0087-0.06480.07260.20290.03560.0573-0.1069-0.1762-0.0269-0.06130.0511-0.0155-0.0736-0.0289-0.0959-68.173651.309638.0383
71.7395-0.38360.52061.42360.3591.02190.06940.24090.1953-0.2463-0.07640.0109-0.19940.0080.007-0.07110.02160.0202-0.07240.0336-0.0913-43.241918.422682.4395
82.3604-1.2249-0.22961.47980.18910.3775-0.01810.0757-0.13580.0649-0.00920.03410.04280.03410.0274-0.12460-0.0114-0.1119-0.0213-0.1101-30.4784-6.926788.6137
92.80850.21490.72642.29731.17932.73330.17310.5316-0.4911-0.2223-0.26020.14540.1332-0.13850.0871-0.0020.0991-0.02170.1577-0.190.0587-22.3636-25.860469.3142
101.2239-0.0205-0.53831.33080.39581.1662-0.02960.1249-0.1841-0.14660.00960.05490.047-0.12140.02-0.08120.0171-0.0014-0.105-0.0065-0.0911-93.131511.699284.0175
110.54430.4253-0.13191.9555-0.23240.48040.0175-0.02940.02240.0687-0.0507-0.0045-0.090.05180.0331-0.09970.0140.0122-0.1097-0.0067-0.1289-78.704236.191590.042
122.3079-0.0742-0.93882.04340.11332.5414-0.02930.00160.1372-0.19370.0472-0.0932-0.12070.168-0.0179-0.0089-0.0426-0.0111-0.08780.0211-0.1145-67.093652.678470.321
131.51880.2050.78090.78440.05341.09070.0691-0.16770.05250.0969-0.0824-0.0686-0.0541-0.02790.0133-0.1094-0.031-0.0061-0.07970.0041-0.1089-91.322619.500522.5688
141.37330.8892-0.10421.5698-0.09810.47110.027-0.0321-0.08190.0215-0.0448-0.03410.0548-0.02880.0178-0.0975-0.0098-0.0287-0.09210.0155-0.1063-104.5924-5.595716.2833
152.2347-0.64291.14162.5881-1.52363.7590.008-0.297-0.23670.3241-0.03760.0210.01030.04830.02950.0504-0.06450.0246-0.04060.0478-0.0331-111.5409-24.800835.893
161.28740.4279-0.49141.2034-0.58381.2336-0.04350.2043-0.0235-0.12260.0551-0.1550.0440.0442-0.0116-0.111-0.02160.034-0.0852-0.0116-0.0839-61.7274-32.095681.3605
172.38610.5042-0.52540.5521-0.06480.4260.01440.22180.1096-0.00980.02640.0545-0.0471-0.1413-0.0408-0.09890.01320.0186-0.06080.049-0.1041-89.8179-28.783387.4828
181.3367-0.0061-0.51841.6371-0.88953.50390.01320.54560.1669-0.3020.12720.1873-0.2087-0.5159-0.14040.00470.071-0.04730.31960.08390.0382-109.8998-24.166168.0974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 249
2X-RAY DIFFRACTION2A250 - 461
3X-RAY DIFFRACTION3A462 - 613
4X-RAY DIFFRACTION4C10 - 249
5X-RAY DIFFRACTION5C250 - 461
6X-RAY DIFFRACTION6C462 - 613
7X-RAY DIFFRACTION7E10 - 249
8X-RAY DIFFRACTION8E250 - 461
9X-RAY DIFFRACTION9E462 - 613
10X-RAY DIFFRACTION10G10 - 249
11X-RAY DIFFRACTION11G250 - 461
12X-RAY DIFFRACTION12G462 - 613
13X-RAY DIFFRACTION13I10 - 249
14X-RAY DIFFRACTION14I250 - 461
15X-RAY DIFFRACTION15I462 - 613
16X-RAY DIFFRACTION16K10 - 249
17X-RAY DIFFRACTION17K250 - 461
18X-RAY DIFFRACTION18K462 - 613

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