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- PDB-2zp3: Carboxylic ester hydrolase, single mutant d49n of bovine pancreat... -

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Basic information

Entry
Database: PDB / ID: 2zp3
TitleCarboxylic ester hydrolase, single mutant d49n of bovine pancreatic pla2 enzyme
ComponentsPhospholipase A2
KeywordsHYDROLASE / ACTIVE SITE MUTANT / METAL BINDING PROTEIN / Calcium / Lipid degradation / Metal-binding / Pyrrolidone carboxylic acid / Secreted
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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process ...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 / calcium-dependent phospholipase A2 activity / phosphatidylcholine metabolic process / 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
AuthorsKanaujia, S.P. / Sekar, K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structures and molecular-dynamics studies of three active-site mutants of bovine pancreatic phospholipase A(2)
Authors: Kanaujia, S.P. / Sekar, K.
History
DepositionJun 27, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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 1.3Nov 1, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1255
Polymers13,8101
Non-polymers3164
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.786, 45.786, 101.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 13809.519 Da / Num. of mol.: 1 / Mutation: D49N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Strain: PANCREAS / Gene: PLA2G1B / Plasmid: PTOA2MBL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00593, phospholipase A2

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Non-polymers , 5 types, 143 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 5mm CACL2, 50mm tris buffer, 70% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 9760 / % possible obs: 94.8 % / Redundancy: 11.98 % / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.055 / Rsym value: 0.056
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.152 / Mean I/σ(I) obs: 24 / Num. unique all: 918 / Rsym value: 0.173 / % possible all: 93.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MKT

1mkt


Resolution: 1.9→22.89 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1373399.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1004 10.3 %RANDOM
Rwork0.191 ---
obs0.191 9704 94.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8751 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å20 Å20 Å2
2--2.44 Å20 Å2
3----4.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.9→22.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 18 139 1114
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 147 9.6 %
Rwork0.223 1392 -
obs--92.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramion.top
X-RAY DIFFRACTION3ion.paramwater_protin.top
X-RAY DIFFRACTION4ligand.paramligand.top

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