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- PDB-7ezz: Crystal structure of Salmonella typhi outer membrane phospholipas... -

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Basic information

Entry
Database: PDB / ID: 7ezz
TitleCrystal structure of Salmonella typhi outer membrane phospholipase (OMPLA) dimer with bound calcium
ComponentsPhospholipase A1
KeywordsHYDROLASE / Outer membrane phospholipase / OMPLA / Outer membrane protein / Calcium-binding / beta-barrel / MEMBRANE PROTEIN
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / phospholipase A2 activity / phospholipase A2 / lipid catabolic process / cell outer membrane ...phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A1 / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / phospholipase A2 activity / phospholipase A2 / lipid catabolic process / cell outer membrane / membrane => GO:0016020 / metal ion binding
Similarity search - Function
Phospholipase A1 / Phospholipase A1 superfamily / Phospholipase A1
Similarity search - Domain/homology
DODECANE / Phospholipase A1
Similarity search - Component
Biological speciesSalmonella typhi (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.76 Å
AuthorsPerumal, P. / Raina, R. / Sreeshma, N.S. / Arockiasamy, A. / Sundarabaalaji, N.
Funding support India, 4items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR13735/BRB/10/786/2011 and BT/PR28080/BID/7/836/2018. India
Department of Science & Technology (DST, India)PDF/2016/003347 India
Department of Biotechnology (DBT, India)BT/PR8636/BRB/10/530/2007 India
Department of Biotechnology (DBT, India)BT/PR10275/GBD/27/88/2007 India
CitationJournal: To Be Published
Title: Crystal structure of Salmonella typhi outer membrane phospholipase (OMPLA) dimer with bound calcium
Authors: Perumal, P. / Raina, R. / Sreeshma, N.S. / Arockiasamy, A. / Sundarabaalaji, N.
History
DepositionJun 2, 2021Deposition site: PDBJ / Processing site: PDBJ
SupersessionJun 23, 2021ID: 5DQX
Revision 1.0Jun 23, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A1
B: Phospholipase A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,72410
Polymers59,1332
Non-polymers1,5908
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-29 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.584, 83.448, 95.644
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: PHE / End label comp-ID: PHE / Auth seq-ID: 33 - 289 / Label seq-ID: 1 - 257

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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Components

#1: Protein Phospholipase A1 / Detergent-resistant phospholipase A / DR-phospholipase A / Outer membrane phospholipase A / OM PLA ...Detergent-resistant phospholipase A / DR-phospholipase A / Outer membrane phospholipase A / OM PLA / Phosphatidylcholine 1-acylhydrolase


Mass: 29566.723 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhi (bacteria) / Gene: pldA, STY3602, t3340 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express Iq
References: UniProt: P0A232, phospholipase A1, phospholipase A2
#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.: 4 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-D12 / DODECANE


Mass: 170.335 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.18 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M sodium iodide, 0.1 M sodium phosphate (pH 7.0), and 33% v/v PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.654→62.879 Å / Num. obs: 17368 / % possible obs: 95.6 % / Redundancy: 6.3 % / CC1/2: 0.991 / Rmerge(I) obs: 0.249 / Rpim(I) all: 0.106 / Rrim(I) all: 0.271 / Net I/σ(I): 7.4 / Num. measured all: 109007
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.654-2.71360.93152178690.7210.3961.014296.6
7.653-62.8795.70.06749238670.9990.0310.07416.298.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROC1.0.5data processing
autoPROC1.0.5data scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QD6

1qd6


Resolution: 2.76→47.87 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.851 / SU B: 16.311 / SU ML: 0.323 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2717 802 4.8 %RANDOM
Rwork0.2244 ---
obs0.2266 16069 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 91.73 Å2 / Biso mean: 29.007 Å2 / Biso min: 5.53 Å2
Baniso -1Baniso -2Baniso -3
1-4.66 Å20 Å2-0 Å2
2---2.63 Å2-0 Å2
3----2.03 Å2
Refinement stepCycle: final / Resolution: 2.76→47.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4077 0 96 54 4227
Biso mean--34.39 21.47 -
Num. residues----511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0124274
X-RAY DIFFRACTIONr_angle_refined_deg1.481.6615814
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8065507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29922.622225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.67315616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2191522
X-RAY DIFFRACTIONr_chiral_restr0.1050.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023322
Refine LS restraints NCS

Ens-ID: 1 / Number: 8177 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.762→2.833 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 63 -
Rwork0.275 1164 -
all-1227 -
obs--100 %

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