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- PDB-4gw3: Crystal Structure of the Lipase from Proteus mirabilis -

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Basic information

Entry
Database: PDB / ID: 4gw3
TitleCrystal Structure of the Lipase from Proteus mirabilis
ComponentsPutative lipase
KeywordsHYDROLASE / lipase
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
ISOPROPYL ALCOHOL / Lipase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKorman, T.P.
CitationJournal: Plos One / Year: 2012
Title: Crystal Structure of Proteus mirabilis Lipase, a Novel Lipase from the Proteus/Psychrophilic Subfamily of Lipase Family I.1.
Authors: Korman, T.P. / Bowie, J.U.
History
DepositionAug 31, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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: Putative lipase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5607
Polymers33,8511
Non-polymers7096
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.438, 65.438, 63.966
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative lipase


Mass: 33851.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Strain: Hauser D1 / 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 , 5 types, 198 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#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.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 5.6
Details: 0.095 M Sodium citrate tribasic dihydrate pH 5.6, 19% v/v 2-Propanol, 19% w/v PEG 4000, 5% glycerol, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.502 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Dec 16, 2009 / Details: varimax confocal optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.502 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 20166 / % possible obs: 97.7 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.137 / Χ2: 1.129 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.80.4319771.215196.2
2.07-2.153.80.35219561.257196.4
2.15-2.253.80.30720301.276196.8
2.25-2.373.80.26220061.235197.1
2.37-2.523.80.22520221.102197.9
2.52-2.713.80.220321.018197.9
2.71-2.993.80.16420221.024198.3
2.99-3.423.70.13120340.959198.5
3.42-4.313.60.10320281.046198.7
4.31-503.70.0820591.161199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.38 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å32.72 Å
Translation2.5 Å32.72 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.2079 / WRfactor Rwork: 0.1778 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8975 / SU B: 6.308 / SU ML: 0.093 / SU R Cruickshank DPI: 0.1748 / SU Rfree: 0.1421 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 1042 5.2 %RANDOM
Rwork0.1672 ---
obs0.1686 19181 97.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.74 Å2 / Biso mean: 28.548 Å2 / Biso min: 9.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å2-0 Å2
2--0.02 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 41 192 2444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0192293
X-RAY DIFFRACTIONr_bond_other_d0.0010.022175
X-RAY DIFFRACTIONr_angle_refined_deg0.8711.9553095
X-RAY DIFFRACTIONr_angle_other_deg0.69734992
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8535282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32124.862109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77115366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.787159
X-RAY DIFFRACTIONr_chiral_restr0.0520.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022622
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02541
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 82 -
Rwork0.206 1385 -
all-1467 -
obs--95.51 %
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)
11.1533-0.044-0.07820.88190.04262.0531-0.0554-0.05060.0957-0.0316-0.05640.20880.0346-0.19780.11170.0278-0.024-0.01540.0712-0.01420.11511.48214.069-0.604
23.7988-1.46571.77473.1883-1.2022.2931-0.1917-0.0626-0.05730.06380.12170.10870.03-0.11390.07010.0563-0.04720.00180.087-0.01890.06186.519.305-3.451
38.6386-2.36765.67044.1196-1.30975.93010.18130.2842-0.0643-0.2287-0.2228-0.01220.19520.09670.04150.0464-0.02610.01870.0925-0.02220.03984.9335.78-14.17
41.1087-0.06290.90950.6821-0.45631.2839-0.03240.07790.04830.00910.05160.0128-0.02710.022-0.01920.0731-0.01320.0040.08010.0060.087715.85612.297-4.494
513.5476-0.0423-3.292113.88510.465420.21070.44290.7931-0.83490.2632-0.56870.20820.7464-0.42890.12570.1093-0.0127-0.03750.0988-0.03090.080224.152.65616.072
613.0914-4.09560.57523.2907-0.03691.87760.0117-0.3379-0.03930.387-0.0373-0.08250.161-0.11340.02560.1257-0.0758-0.01730.09550.01790.008919.2516.90322.127
70.0917-0.43021.14292.461-5.063816.38590.0022-0.133-0.05790.5410.42810.10890.7133-1.1539-0.43020.7567-0.1861-0.05810.58120.1190.46118.3363.25417.736
88.11352.7704-4.29121.7032-2.14237.6481-0.0377-0.2373-0.4131-0.088-0.0504-0.14420.30850.28580.08810.07910.0141-0.01440.04640.00020.076223.265.3673.102
97.1012-3.5098-0.8622.48621.75554.7632-0.00350.1534-0.0898-0.19140.0174-0.1779-0.01670.2075-0.0140.1015-0.03880.09960.11490.01580.139826.18412.098-8.072
109.8032.00127.52425.97053.936813.5534-0.00710.13740.127-0.06810.1159-0.3265-0.14030.2165-0.10880.0826-0.02420.03320.08530.05180.088622.69521.019-10.886
110.47360.60510.32391.70412.47545.2040.11310.0940.25890.06370.10740.0859-0.065-0.1617-0.22050.13110.0110.02590.1011-0.00470.288316.75124.0212.569
124.25046.09681.676715.08952.64612.26270.0337-0.73160.34270.6408-0.27320.5073-0.1821-0.36490.23940.11520.05370.02670.263-0.09180.08297.58424.85519.853
135.5807-0.6957-3.2042.41220.11852.8189-0.0785-0.1662-0.08310.10520.02-0.14260.252-0.1030.05850.0795-0.0436-0.02560.1182-0.02070.034620.32618.87416.628
141.51410.06980.21340.65340.43931.2182-0.016-0.12880.27350.0158-0.07770.0612-0.1356-0.02590.09380.0671-0.0043-0.01030.0565-0.02550.121411.97823.3255.865
156.53610.282.0345.77333.080219.5217-0.18810.2590.8724-0.26640.3863-0.073-0.70140.1879-0.19820.1001-0.0358-0.05450.0540.06380.19847.86326.924-11.849
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 53
3X-RAY DIFFRACTION3A54 - 71
4X-RAY DIFFRACTION4A72 - 114
5X-RAY DIFFRACTION5A115 - 119
6X-RAY DIFFRACTION6A120 - 142
7X-RAY DIFFRACTION7A143 - 154
8X-RAY DIFFRACTION8A155 - 169
9X-RAY DIFFRACTION9A170 - 178
10X-RAY DIFFRACTION10A179 - 192
11X-RAY DIFFRACTION11A193 - 202
12X-RAY DIFFRACTION12A203 - 215
13X-RAY DIFFRACTION13A216 - 230
14X-RAY DIFFRACTION14A231 - 276
15X-RAY DIFFRACTION15A277 - 287

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