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- PDB-1fw2: OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1fw2
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: 2.6 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: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)31,5772
Polymers31,5371
Non-polymers401
Water90150
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.532, 77.532, 100.525
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121

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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: 31536.875 Da / Num. of mol.: 1 / Fragment: OMPLA WITH N-TERMINAL EXTENSION / Mutation: ARIRAP EXTENSION
Source method: isolated from a genetically manipulated source
Details: COVALENTLY SULFONYLATED ON SERINE144 / Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A921, phospholipase A1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.76 Å3/Da / Density % sol: 55.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: MPD, calcium chloride, Bis-Tris, pH 5.9, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Temperature: 22 ℃ / Details: Blaauw, M., (1995) FEBS Lett., 373, 10.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124-28 %(v/v)MPD1reservoir
2100 mMBis-Tris1reservoir
31 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1
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: 2.6→30 Å / Num. all: 9975 / Num. obs: 9975 / % possible obs: 89.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.034 / Net I/σ(I): 37.3
Reflection shellResolution: 2.6→2.64 Å / Rmerge(I) obs: 0.084 / % possible all: 62.3
Reflection
*PLUS
Lowest resolution: 30 Å / Num. measured all: 47201
Reflection shell
*PLUS
% possible obs: 62.3 % / Mean I/σ(I) obs: 10.3

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.6→30 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: anisotropic scaling and bulk solvent correction applied
RfactorNum. reflection% reflectionSelection details
Rfree0.298 947 9.5 %RANDOM
Rwork0.222 ---
all0.222 9975 --
obs-9959 89.2 %-
Displacement parametersBiso mean: 49.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.77 Å20 Å2
2--0.34 Å20 Å2
3----0.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 1 50 2145
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d26.9
X-RAY DIFFRACTIONx_improper_angle_d1.23
LS refinement shellResolution: 2.6→2.69 Å / Rfactor Rfree error: 0.051 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.385 57 8.1 %
Rwork0.336 645 -
obs--64.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 9.5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 49.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.23
LS refinement shell
*PLUS
Rfactor Rfree: 0.385 / % reflection Rfree: 8.1 % / Rfactor Rwork: 0.336 / Rfactor obs: 0.336

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