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- PDB-2bd1: A possible role of the second calcium ion in interfacial binding:... -

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Basic information

Entry
Database: PDB / ID: 2bd1
TitleA possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2
ComponentsPhospholipase A2
KeywordsHYDROLASE / alpha helix / beta sheet
Function / homology
Function and homology information


Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity ...Acyl chain remodelling of PS / Acyl chain remodelling of PG / Synthesis of PA / Acyl chain remodelling of PC / Acyl chain remodelling of PE / Acyl chain remodelling of PI / positive regulation of podocyte apoptotic process / phosphatidylglycerol metabolic process / phosphatidylcholine metabolic process / calcium-dependent phospholipase A2 activity / phospholipase A2 / bile acid binding / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / innate immune response in mucosa / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-positive bacterium / signaling receptor binding / calcium ion binding / cell surface / extracellular space
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSekar, K. / Velmurugan, D. / Tsai, M.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Suggestive evidence for the involvement of the second calcium and surface loop in interfacial binding: monoclinic and trigonal crystal structures of a quadruple mutant of phospholipase A(2).
Authors: Sekar, K. / Yogavel, M. / Kanaujia, S.P. / Sharma, A. / Velmurugan, D. / Poi, M.J. / Dauter, Z. / Tsai, M.D.
History
DepositionOct 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: reflns_shell / software
Item: _reflns_shell.number_unique_all / _reflns_shell.percent_possible_all
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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.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.pdbx_dist_value / _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 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0348
Polymers27,6372
Non-polymers3976
Water3,927218
1
A: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0174
Polymers13,8191
Non-polymers1983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0174
Polymers13,8191
Non-polymers1983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.58, 48.69, 67.55
Angle α, β, γ (deg.)90, 102.3, 90
Int Tables number5
Space group name H-MC121
DetailsThere are two monomers (same copy) are in the asymmmetryic unit. The biological assembly itself is a monomer

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Components

#1: Protein Phospholipase A2 / / Phosphatidylcholine 2-acylhydrolase / Group IB phospholipase A2


Mass: 13818.567 Da / Num. of mol.: 2 / Mutation: K53M, K56M, K120M, K121M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PLA2G1B / Plasmid: PTO-A2MBL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P00593, phospholipase A2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.17 Å3/Da / Density % sol: 43.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.2
Details: The crystallization droplet contained 5 micro litre of protein (18 to 20 mg/ml) in 50 mM tris buffer with 2 micro litre of MPD (60%) and the reservoir contained 70% of MPD., pH 7.2, VAPOR ...Details: The crystallization droplet contained 5 micro litre of protein (18 to 20 mg/ml) in 50 mM tris buffer with 2 micro litre of MPD (60%) and the reservoir contained 70% of MPD., pH 7.2, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→14.69 Å / Num. all: 13356 / Num. obs: 13356 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Rmerge(I) obs: 0.093
Reflection shellResolution: 1.9→1.99 Å / Rmerge(I) obs: 0.458 / Num. unique all: 1507

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UNE, 1MKT

1une

1mkt


Resolution: 1.9→14.69 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 1071 -RANDOM
Rwork0.207 ---
obs-13340 94.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å2-0.28 Å2
2--0.49 Å20 Å2
3----0.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 4 234 2144
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.026
RfactorNum. reflection% reflection
Rfree0.299 131 -
Rwork0.298 --
obs-1507 70.1 %

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