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- PDB-4gxn: Diethylphosphonate Inhibited Structure of the Proteus mirabilis Lipase -

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Basic information

Entry
Database: PDB / ID: 4gxn
TitleDiethylphosphonate Inhibited Structure of the Proteus mirabilis Lipase
ComponentsPutative lipase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / lipase / hydrolase / a/b hydrolase fold / HYDROLASE-HYDROLASE INHIBITOR complex
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
DIETHYL PHOSPHONATE / TRIETHYLENE GLYCOL / Lipase
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsKorman, T.P. / Bowie, J.U.
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
DepositionSep 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 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 / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_conn_type.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)34,1794
Polymers33,8511
Non-polymers3283
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.574, 65.574, 63.465
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#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: ATCC / Gene: LipA / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Gold(DE3) / References: UniProt: B4EVM3, triacylglycerol lipase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-DEP / DIETHYL PHOSPHONATE


Mass: 138.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H11O3P
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.15 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Bis-Tris propane pH 6.5, 16% w/v PEG 2000 MME, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Mar 21, 2011 / Details: varimax confocal optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 20700 / Num. obs: 20659 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.125 / Χ2: 1.058 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.10.53220781.088199.9
2.07-2.153.10.41420421.082199.9
2.15-2.253.10.32420821.11100
2.25-2.373.10.26220741.1191100
2.37-2.523.10.20720661.033199.9
2.52-2.713.20.17420771.046199.9
2.71-2.993.20.14120701.027199.9
2.99-3.423.20.10920361.0631100
3.42-4.313.20.09920770.997199.9
4.31-503.20.08720571.036199

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→32.79 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2453 / WRfactor Rwork: 0.1894 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8367 / SU B: 12.854 / SU ML: 0.175 / SU R Cruickshank DPI: 0.3731 / SU Rfree: 0.2471 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.373 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.249 715 5.2 %RANDOM
Rwork0.1954 ---
obs0.1982 13875 89.55 %-
all-15495 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.39 Å2 / Biso mean: 32.802 Å2 / Biso min: 9.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.06 Å2-0 Å2
2---0.06 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 19 175 2405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0192273
X-RAY DIFFRACTIONr_bond_other_d0.0010.022144
X-RAY DIFFRACTIONr_angle_refined_deg0.8721.9483066
X-RAY DIFFRACTIONr_angle_other_deg0.70334914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1015282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82624.815108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.574159
X-RAY DIFFRACTIONr_chiral_restr0.0530.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022617
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 53 -
Rwork0.239 863 -
all-916 -
obs--82.08 %
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)
12.8512-0.6006-1.00581.39920.41673.0733-0.0511-0.13580.0032-0.0671-0.12260.47640.168-0.20180.17360.0472-0.0435-0.03770.099-0.04630.18891.36514.155-0.373
24.8764-1.46452.35973.4195-1.31142.2552-0.0140.1685-0.03830.0568-0.1670.10040.0339-0.05030.1810.1213-0.0077-0.00550.0984-0.03180.05417.5718.223-3.494
32.5543-0.0811.96841.37640.48362.3853-0.00120.19090.0414-0.0979-0.0320.0021-0.02270.01140.03310.0986-0.01490.03450.10580.0170.036612.57510.398-7.278
412.2233-6.8093.498319.0885-1.979133.00550.8868-0.1509-0.3760.1461-0.8485-0.7341.4524-0.3263-0.03830.2634-0.0873-0.02510.10350.09120.130425.8951.88817.673
57.0624-6.70693.40056.5217-3.20197.44620.8078-0.4254-0.617-0.45180.13240.58811.2602-0.971-0.94020.9212-0.7009-0.15280.55250.11280.122714.67.4221.531
64.18330.5614-2.88311.9884-1.89888.971-0.12590.0056-0.303-0.0645-0.0621-0.23460.36570.21770.1880.1039-0.0008-0.00250.09910.00730.14124.1486.342-0.484
74.56581.7991-0.1617.08890.96334.2772-0.21870.34190.523-0.229-0.0249-0.5026-0.30890.47520.24360.1193-0.0661-0.00830.16710.11270.185122.95120.64-9.013
84.3480.40430.79031.954-0.92842.8306-0.0222-0.55710.48010.2591-0.22170.1464-0.1653-0.18430.24390.1259-0.04250.01590.1455-0.11850.101611.93923.72316.914
92.086-0.62560.51932.08730.30082.9014-0.1036-0.08230.28210.1091-0.016-0.2177-0.22680.07510.11960.0904-0.0512-0.03170.0709-0.01620.090818.62121.8747.368
102.6107-0.17150.53391.54-0.34157.6056-0.1428-0.04740.8004-0.1434-0.09910.23-0.5034-0.1240.24190.09270.0103-0.08990.0751-0.04140.30336.15526.248-0.422
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 33
2X-RAY DIFFRACTION2A34 - 55
3X-RAY DIFFRACTION3A56 - 114
4X-RAY DIFFRACTION4A115 - 123
5X-RAY DIFFRACTION5A124 - 154
6X-RAY DIFFRACTION6A155 - 175
7X-RAY DIFFRACTION7A176 - 195
8X-RAY DIFFRACTION8A196 - 223
9X-RAY DIFFRACTION9A224 - 259
10X-RAY DIFFRACTION10A260 - 287

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