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- PDB-1fw3: OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1fw3
TitleOUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI
ComponentsOUTER MEMBRANE PHOSPHOLIPASE A
Keywordshydrolase / membrane protein / ANTI-PARALLEL BETA BARREL DIMER
Function / homology
Function and homology information


phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / phospholipase activity / phosphatidylglycerol metabolic process / lysophospholipase activity / phospholipase A2 activity / phospholipase A2 / lipid catabolic process ...phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / phospholipase activity / phosphatidylglycerol metabolic process / lysophospholipase activity / phospholipase A2 activity / phospholipase A2 / 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 / Resolution: 2.8 Å
AuthorsSnijder, H.J. / Kingma, R.L. / Kalk, K.H. / Dekker, N. / Egmond, M.R. / Dijkstra, B.W.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Structural investigations of calcium binding and its role in activity and activation of outer membrane phospholipase A from Escherichia coli.
Authors: Snijder, H.J. / 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. / Kalk, K.H. / Verheij, H.M. / Dijkstra, B.W.
#3: Journal: Biochim.Biophys.Acta / Year: 2000
Title: Bacterial phospholipase A: structure and function of an integral membrane phospholipase
Authors: Snijder, H.J. / Dijkstra, B.W.
History
DepositionSep 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OUTER MEMBRANE PHOSPHOLIPASE A
B: OUTER MEMBRANE PHOSPHOLIPASE A


Theoretical massNumber of molelcules
Total (without water)63,6512
Polymers63,6512
Non-polymers00
Water00
1
A: OUTER MEMBRANE PHOSPHOLIPASE A


Theoretical massNumber of molelcules
Total (without water)31,8251
Polymers31,8251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: OUTER MEMBRANE PHOSPHOLIPASE A


Theoretical massNumber of molelcules
Total (without water)31,8251
Polymers31,8251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.540, 84.970, 95.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsThis enzyme is regulated by reversible dimerisation

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Components

#1: Protein OUTER MEMBRANE PHOSPHOLIPASE A / E.C.3.1.1.32 / OMPLA / DETERGENT-RESISTANT PHOSPHOLIPASE A / DR-PHOSPHOLIPASE A / PHOSPHATIDYLCHOLINE 1-ACYLHYDROLASE


Mass: 31825.363 Da / Num. of mol.: 2 / Fragment: OMPLA WITH N-TERMINAL EXTENSION / Mutation: ARIRAP EXTENSION
Source method: isolated from a genetically manipulated source
Details: COVALENTLY SULFONYLATED ON SERINE144, RESIDUE S1H / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A921, phospholipase A1

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: b-OG, Tris, Potassium Chloride, Ammonium phosphate, pH 6.6, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mg/mlprotein1drop
21.95 %(w/v)beta-OG1drop
310 mM1dropKCl
42 mMTris1drop
512-17 %(v/v)PEG4001reservoircan be replaced by 0.25M ammonium phosphate

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8342
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8342 Å / Relative weight: 1
ReflectionResolution: 2.79→37.9 Å / Num. all: 14611 / Num. obs: 14611 / % possible obs: 81 % / Redundancy: 3.7 % / Biso Wilson estimate: 40 Å2 / Rmerge(I) obs: 0.121 / Net I/σ(I): 8.3
Reflection shellResolution: 2.79→2.9 Å / Rmerge(I) obs: 0.286 / % possible all: 53.5
Reflection
*PLUS
Num. measured all: 53984
Reflection shell
*PLUS
% possible obs: 53.5 % / Mean I/σ(I) obs: 2.9

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.8→37.9 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: anisotropic scaling and bulk solvent correction applied
RfactorNum. reflection% reflectionSelection details
Rfree0.281 980 6.7 %RANDOM
Rwork0.224 ---
obs-14611 81 %-
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.87 Å20 Å20 Å2
2--0.17 Å20 Å2
3---0.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.8→37.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4102 0 0 0 4102
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_improper_angle_d1.19
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.083 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.332 16 4.2 %
Rwork0.247 362 -
obs--20.3 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 6.7 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor Rfree: 0.332 / % reflection Rfree: 4.2 % / Rfactor Rwork: 0.247 / Rfactor obs: 0.247

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