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- PDB-1qd5: OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1qd5
TitleOUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI
ComponentsOUTER MEMBRANE PHOSPHOLIPASE A
KeywordsMEMBRANE PROTEIN / ANTI-PARALLEL BETA BARREL / membrane phospholipase
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: 2.17 Å
AuthorsSnijder, H.J. / Ubarretxena-Belandia, I. / Blaauw, M. / Kalk, K.H. / Verheij, H.M. / Egmond, M.R. / Dekker, N. / Dijkstra, B.W.
Citation
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.
#1: 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
DepositionJul 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Apr 4, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.6Apr 11, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.7Jul 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 1.8Feb 14, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)32,9996
Polymers31,5371
Non-polymers1,4625
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.55, 78.55, 101.52
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a monomer

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Components

#1: Protein OUTER MEMBRANE PHOSPHOLIPASE A


Mass: 31536.875 Da / Num. of mol.: 1 / Mutation: N-TERMINAL EXTENSION ARIRAP
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Description: ESCHERICHIA COLI, OUTER MEMBRANE / 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 / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 29% MPD, 0.1 M Bis-Tris, 1 mM calciumchloride, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion
Details: protein solution is mixed in a 3:2 ratio with well solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
210 mMsuccinate1drop
31.5 %beta-OG1drop
41 mM1dropNaN3
525-29 %(v/v)MPD1reservoir
61 mM1reservoirCaCl2
70.1 Mbis-Tris 1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11201
21201
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONEMBL/DESY, HAMBURG X1110.9164
SYNCHROTRONESRF BM0220.9901
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEMay 16, 1996
MARRESEARCH2CCDFeb 7, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91641
20.99011
ReflectionResolution: 2.17→37 Å / Num. all: 225025 / Num. obs: 15058 / % possible obs: 76.6 % / Redundancy: 14.9 % / Biso Wilson estimate: 44.5 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 15
Reflection shellResolution: 2.17→2.25 Å / Rmerge(I) obs: 0.21 / Num. unique all: 254 / % possible all: 14.4
Reflection shell
*PLUS
% possible obs: 14.4 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
DMmodel building
X-PLOR3.843refinement
DENZOdata reduction
XDSdata reduction
SCALEPACKdata scaling
XDSdata scaling
DMphasing
RefinementResolution: 2.17→36.6 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: RESOLUTION-DEPENDENT WEIGHTING SCHEME BULK SOLVENT CORRECTION
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1389 9.2 %RANDOM
Rwork0.221 ---
obs0.221 15058 76.6 %-
Displacement parametersBiso mean: 56 Å2
Baniso -1Baniso -2Baniso -3
1-5.95 Å27.21 Å20 Å2
2--5.95 Å20 Å2
3----11.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.17→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 82 28 2204
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.93
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.213.5
X-RAY DIFFRACTIONx_mcangle_it3.445
X-RAY DIFFRACTIONx_scbond_it3.165
X-RAY DIFFRACTIONx_scangle_it4.235.5
LS refinement shellResolution: 2.17→2.25 Å / Rfactor Rfree error: 0.078 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.39 25 9 %
Rwork0.26 254 -
obs--14.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.WATTOPH19.SOL
X-RAY DIFFRACTION3PARAM_BOG.DATTOPOL_BOG_MOD.DAT

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