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- PDB-4hs9: Methanol tolerant mutant of the Proteus mirabilis lipase -

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Basic information

Entry
Database: PDB / ID: 4hs9
TitleMethanol tolerant mutant of the Proteus mirabilis lipase
ComponentsLipase
KeywordsHYDROLASE / lipase / alpha/beta hydrolase
Function / homology
Function and homology information


triacylglycerol lipase / triacylglycerol lipase activity / metal ion binding
Similarity search - Function
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
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsKorman, T.P.
CitationJournal: Biotechnol Biofuels / Year: 2013
Title: Dieselzymes: development of a stable and methanol tolerant lipase for biodiesel production by directed evolution.
Authors: Korman, T.P. / Sahachartsiri, B. / Charbonneau, D.M. / Huang, G.L. / Beauregard, M. / Bowie, J.U.
History
DepositionOct 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _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.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_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)34,6736
Polymers33,9131
Non-polymers7605
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.099, 54.849, 96.013
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lipase


Mass: 33913.082 Da / Num. of mol.: 1
Mutation: N17S, R33T, L64I, A70T, M119I, G181C, G202E, K208N, F225L, S238C, I255F, G266S, D270N, Q277L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: ATCC / Gene: LipA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: B4EVM3, triacylglycerol lipase

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Non-polymers , 6 types, 122 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 1.87 Å3/Da / Density % sol: 34.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1X MMT Buffer pH 5.0, 20% PEG1500, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→90 Å / Num. obs: 23372 / % possible obs: 96.6 % / Redundancy: 5.9 % / Rmerge(I) obs: 0.068 / Χ2: 0.998 / Net I/σ(I): 10.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.865.60.29923000.944197
1.86-1.946.30.2123690.999199.7
1.94-2.036.30.15423791.001199.8
2.03-2.136.10.11923591.003199.4
2.13-2.275.90.09523541.001198.2
2.27-2.445.80.07723041.008196.2
2.44-2.696.20.06323850.999198.9
2.69-3.085.80.05323661.007197.3
3.08-3.885.20.04521561.009187.8
3.88-905.50.06424001.003192.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.63 Å
Translation2.5 Å47.63 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→47.63 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.1775 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8875 / SU B: 4.655 / SU ML: 0.074 / SU R Cruickshank DPI: 0.1388 / SU Rfree: 0.1254 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.139 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2052 1184 5.1 %RANDOM
Rwork0.1709 ---
obs0.1726 23320 96.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.61 Å2 / Biso mean: 31.831 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å2-0 Å2
2--0.24 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2237 0 48 117 2402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192329
X-RAY DIFFRACTIONr_bond_other_d0.0010.022207
X-RAY DIFFRACTIONr_angle_refined_deg1.9761.9583146
X-RAY DIFFRACTIONr_angle_other_deg0.9583.0015071
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1625286
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10324.862109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.60315371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.591159
X-RAY DIFFRACTIONr_chiral_restr0.1230.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022650
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 79 -
Rwork0.261 1593 -
all-1672 -
obs--94.36 %
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)
18.38953.26273.045616.866312.698544.2230.20210.3460.4655-0.49670.2968-0.3353-1.98940.7478-0.49880.2563-0.03340.06370.13350.10820.2919-10.43617.966-3.156
23.35230.7297-2.13441.0163-0.06794.28050.05980.16570.05650.1386-0.01920.1601-0.1399-0.3744-0.04060.18180.03860.00960.08820.00990.242-23.3185.8549.586
37.22710.6717-1.003715.27470.02219.91250.0840.43641.1780.3267-0.21760.761-0.765-0.48560.13360.27570.04640.05350.04390.05230.4187-17.54318.5035.384
42.77650.1415-0.82183.6146-1.81643.3114-0.13350.5036-0.2315-0.37740.03880.14950.4057-0.49840.09460.2079-0.0357-0.00880.1733-0.05340.2258-22.658-1.763-1.76
511.4987-1.20831.551811.1598-3.68353.3270.21850.97030.3211-0.1247-0.02730.02450.01810.1526-0.19110.26670.08080.02140.27520.10330.1592-21.24311.744-10.35
62.17210.3961-0.65412.25-1.16574.4486-0.05510.3024-0.22-0.2102-0.0578-0.07420.25030.05890.11290.19510.01770.03830.1152-0.01690.2382-12.5450.553-1.284
75.95227.8233-0.856810.785-1.89024.3266-0.0161-0.0574-0.2734-0.0744-0.0814-0.25150.5224-0.03030.09750.37680.06760.07110.02310.04570.3739-15.845-18.81113.043
810.55116.829811.238916.544520.138156.73280.03520.1625-0.719-0.21420.6620.06511.23990.8924-0.69720.39090.03330.12310.03350.04070.4215-17.751-25.96718.996
98.6386-9.17711.096617.8289-4.77663.95830.1835-0.00730.019-0.2292-0.11710.3099-0.1001-0.0756-0.06640.2963-0.03020.05710.01820.01050.2902-23.89-11.43821.88
104.62520.5599-4.86344.3767-3.10177.915-0.38970.6012-0.9834-0.4151-0.00560.10871.0881-0.31590.39540.49960.04920.06510.1542-0.20420.5737-15.276-13.4442.265
110.45210.936-0.3252.2831-0.70737.9039-0.05920.0312-0.316-0.1356-0.1173-0.55240.35581.230.17650.18580.09520.07660.35590.00680.3831-1.596-0.6050.701
126.9381-0.2675-4.59792.99250.10367.870.0514-1.238-0.07480.5422-0.1658-0.282-0.43771.00670.11440.3424-0.0835-0.05710.2510.07370.2651-10.8350.73626.732
1328.6598-17.128-3.69925.2049-0.21680.8729-0.0621-0.80710.15741.03580.0431-0.1692-0.14310.18060.01890.3383-0.05630.04250.13130.03290.3151-15.998-4.45925.073
141.46880.5126-1.14622.141-0.62593.4283-0.0274-0.1289-0.30480.1354-0.2095-0.26070.23110.53570.23690.18030.05670.00440.14370.10550.3276-5.742-4.77914.801
152.86732.1882-3.10542.5972-3.71115.71110.1563-0.15580.00290.2271-0.2375-0.1035-0.35830.4060.08130.2342-0.0487-0.00140.08380.01980.2236-10.7899.66512.808
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 5
2X-RAY DIFFRACTION2A6 - 31
3X-RAY DIFFRACTION3A32 - 38
4X-RAY DIFFRACTION4A39 - 60
5X-RAY DIFFRACTION5A61 - 71
6X-RAY DIFFRACTION6A72 - 107
7X-RAY DIFFRACTION7A108 - 119
8X-RAY DIFFRACTION8A120 - 127
9X-RAY DIFFRACTION9A128 - 148
10X-RAY DIFFRACTION10A149 - 174
11X-RAY DIFFRACTION11A175 - 198
12X-RAY DIFFRACTION12A199 - 213
13X-RAY DIFFRACTION13A214 - 220
14X-RAY DIFFRACTION14A221 - 254
15X-RAY DIFFRACTION15A255 - 287

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