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- PDB-1ilz: OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI N156A ACTIVE... -

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Basic information

Entry
Database: PDB / ID: 1ilz
TitleOUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI N156A ACTIVE SITE MUTANT pH 6.1
ComponentsOUTER MEMBRANE PHOSPHOLIPASE A
KeywordsHYDROLASE / MEMBRANE PROTEIN / ANTI-PARALLEL BETA BARREL / MEMBRANE PHOSPHOLIPASE / SERINE HYDROLASE / CATALYTIC TRIAD / ASN ALA MUTATION
Function / homology
Function and homology information


phospholipase A1 / phospholipase activity / phospholipase A1 activity / phosphatidylglycerol metabolic process / phospholipase A2 activity / phospholipase A2 / phosphatidylcholine lysophospholipase activity / lipid catabolic process / cell outer membrane / calcium ion binding / protein homodimerization activity
Similarity search - Function
Phospholipase A1 / Phospholipase A1 / Phospholipase A1 superfamily / Phospholipase A1 / Outer membrane phospholipase (ompla); Chain C / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSnijder, H.J. / Van Eerde, J.H. / Kingma, R.L. / Kalk, K.H. / Dekker, N. / Egmond, M.R. / Dijkstra, B.W.
Citation
Journal: Protein Sci. / Year: 2001
Title: Structural investigations of the active-site mutant Asn156Ala of outer membrane phospholipase A: function of the Asn-His interaction in the catalytic triad.
Authors: Snijder, H.J. / Van Eerde, J.H. / Kingma, R.L. / Kalk, K.H. / Dekker, N. / Egmond, M.R. / Dijkstra, B.W.
#1: Journal: Nature / Year: 1999
Title: Structural Evidence for Dimerization-Regulated Activation of an Integral Membrane Phospholipase
Authors: Snijder, H.J. / Ubarretxena-Belandia, I. / Blaauw, M. / Kalk, K.H. / Verheij, H.M. / Egmond, M.R. / Dekker, N. / Dijkstra, B.W.
#2: Journal: FEBS Lett. / Year: 1995
Title: Crystallization and Preliminary X-Ray Analysis of Outer Membrane Phospholipase A from Escherichia Coli
Authors: Blaauw, M. / Dekker, N. / Verheij, H.M. / Kalk, K.H. / Dijkstra, B.W.
History
DepositionMay 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 21, 2022Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN ATOMS C5'-C8' OF BOG 503 LACK INTERPRETABLE ELECTRON DENSITY. ATOMS C3'-C8' OF BOG 504 ...HETEROGEN ATOMS C5'-C8' OF BOG 503 LACK INTERPRETABLE ELECTRON DENSITY. ATOMS C3'-C8' OF BOG 504 HAVE MISSING ELECTRON DENSITY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER MEMBRANE PHOSPHOLIPASE A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1928
Polymers31,4941
Non-polymers1,6987
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.168, 78.168, 101.685
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein OUTER MEMBRANE PHOSPHOLIPASE A / OMPLA / DETERGENT-RESISTANT PHOSPHOLIPASE A / DR-PHOSPHOLIPASE A / PHOSPHATIDYLCHOLINE 1-ACYLHYDROLASE


Mass: 31493.852 Da / Num. of mol.: 1 / Mutation: N156A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pldA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A921, phospholipase A1
#2: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside / Beta-Octylglucoside / octyl beta-D-glucoside / octyl D-glucoside / octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: MPD, calcium chloride, bis-tris buffer, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
127 %(v/v)MPD1reservoir
20.4-1.0 mM1reservoirCaCl2
30.1 MBis-Tris1reservoir
410 mg/mlprotein1drop
510 mM1dropKCl
61 %(w/v)OGP1drop
70.2 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→31 Å / Num. all: 12728 / Num. obs: 150605 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.037 / Rsym value: 0.037 / Net I/σ(I): 39.2
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.113 / Mean I/σ(I) obs: 8.3 / Num. unique all: 611 / Rsym value: 0.113 / % possible all: 96.1
Reflection
*PLUS
Lowest resolution: 31 Å / Num. obs: 12728 / Num. measured all: 150605
Reflection shell
*PLUS
% possible obs: 96.1 % / Num. unique obs: 611

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Processing

Software
NameVersionClassification
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Starting model 1QD5 with the active site residues truncated to ala and all waters and detergent molecules removed. All remaining atoms have been given a random shift of almost 0.5 ...Starting model: Starting model 1QD5 with the active site residues truncated to ala and all waters and detergent molecules removed. All remaining atoms have been given a random shift of almost 0.5 Angstrom in all directions.

1qd5


Resolution: 2.5→31 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: Bulk solvent correction was applied as implemented in CNS bulk solvent: density level= 0.379342 e/A^3, B-factor= 52.8672 A^2
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1231 9.7 %The same test set was used as in the refinement of the native monomer structure 1qd5, which had been selected randomly.
Rwork0.222 ---
all-12884 --
obs-12728 98.8 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.882 Å2-9.735 Å20 Å2
2---8.882 Å20 Å2
3---17.765 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 90 48 2229
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006075
X-RAY DIFFRACTIONc_angle_d1.1358
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 31 Å / σ(F): 0 / % reflection Rfree: 9.7 % / Rfactor obs: 0.222
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.1358
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7

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