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- PDB-1qd6: OUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1qd6
TitleOUTER MEMBRANE PHOSPHOLIPASE A FROM ESCHERICHIA COLI
Components
  • OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)
  • PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))
KeywordsMEMBRANE PROTEIN / ANTI-PARALLEL BETA BARREL DIMER
Function / homology
Function and homology information


phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / : / phospholipase A1 activity / phospholipase activity / phosphatidylglycerol metabolic process / phospholipase A2 activity / lysophospholipase activity / phospholipase A2 / lipid catabolic process ...phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / : / phospholipase A1 activity / phospholipase activity / phosphatidylglycerol metabolic process / phospholipase A2 activity / lysophospholipase 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
1-HEXADECANOSULFONIC ACID / Phospholipase A1
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 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. / Kalk, K.H. / Verheij, H.M. / Dijkstra, B.W.
History
DepositionJul 9, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Structure summary / Category: audit_author / pdbx_unobs_or_zero_occ_residues / Item: _audit_author.name
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_conn_type / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)
B: OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)
C: PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))
D: PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9268
Polymers58,2324
Non-polymers6934
Water1,20767
1
A: OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)
C: PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5035
Polymers29,1162
Non-polymers3873
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-16 kcal/mol
Surface area12210 Å2
MethodPISA
2
B: OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)
D: PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4233
Polymers29,1162
Non-polymers3071
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-15 kcal/mol
Surface area12160 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8400 Å2
ΔGint-57 kcal/mol
Surface area20010 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)80.067, 84.038, 95.245
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer constructed from chain A,C and B,D related by a NCS twofold rotation

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Components

#1: Protein/peptide OUTER MEMBRANE PHOSPHOLIPASE (OMPLA)


Mass: 1402.640 Da / Num. of mol.: 2 / Fragment: RESDIUES 33-45 / Source method: obtained synthetically / References: UniProt: P0A921
#2: Protein PROTEIN (OUTER MEMBRANE PHOSPHOLIPASE (OMPLA))


Mass: 27713.598 Da / Num. of mol.: 2
Mutation: ENZYME WITH N-TERMINAL EXTENSION ARIRAP AND COVALENTLY SULFONYLATED ON SERINE144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P0A921, phospholipase A1
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-HDS / 1-HEXADECANOSULFONIC ACID


Mass: 306.504 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O3S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE N-TERMINAL WAS MUTATED TO EXTEND WITH RESIDUES ARIRAP

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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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: PEG400, pH 6.6, 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
51 mM1reservoirCaCl2
60.1 Mbis-Tris1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID2 / Wavelength: 0.99385
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99385 Å / Relative weight: 1
ReflectionResolution: 2.1→20.3 Å / Num. all: 76223 / Num. obs: 28336 / % possible obs: 74.1 % / Redundancy: 2.69 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.17 Å / Rmerge(I) obs: 0.265 / Num. unique all: 2510 / % possible all: 66.7
Reflection shell
*PLUS
% possible obs: 66.7 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: MONOMER OMPLA (1QD5) WITHOUT WATER/DETERGENT MOLECULES

1qd5


Resolution: 2.1→20.3 Å / Rfactor Rfree error: 0.006 / 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: Bulk solvent correction Anisotropic scaling
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2408 8.3 %RANDOM
Rwork0.226 ---
obs0.226 28947 74.1 %-
Displacement parametersBiso mean: 34.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å20 Å20 Å2
2--0.13 Å20 Å2
3---0.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.1→20.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4111 0 42 67 4220
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_improper_angle_d1.08
X-RAY DIFFRACTIONx_mcbond_it2.42.5
X-RAY DIFFRACTIONx_mcangle_it3.283
X-RAY DIFFRACTIONx_scbond_it5.855
X-RAY DIFFRACTIONx_scangle_it7.285.5
LS refinement shellResolution: 2.1→2.17 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.279 180 7.2 %
Rwork0.225 2330 -
obs--66.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1parhcsdx_adapt.protophcsdx.pro
X-RAY DIFFRACTION2param19.soltoph19.sol
X-RAY DIFFRACTION3hdsf.parhdsf.top
X-RAY DIFFRACTION4ca.parca.top
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.08

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