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- PDB-1ows: Crystal structure of a C49 Phospholipase A2 from Indian cobra rev... -

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Basic information

Entry
Database: PDB / ID: 1ows
TitleCrystal structure of a C49 Phospholipase A2 from Indian cobra reveals carbohydrate binding in the hydrophobic channel
Components(Phospholipase A2) x 2
KeywordsHYDROLASE / Phospholipase / Enzyme / Phospholipids
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / calcium ion binding / extracellular region
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
Acidic phospholipase A2 2
Similarity search - Component
Biological speciesNaja naja (Indian cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsJabeen, T. / Jasti, J. / Singh, N. / Singh, R.K. / Sharma, S. / Kaur, P. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of a C49 Phospholipase A2 from Indian cobra reveals carbohydrate binding in the hydrophobic channel
Authors: Jabeen, T. / Jasti, J. / Singh, N. / Singh, R.K. / Sharma, S. / Kaur, P. / Singh, T.P.
History
DepositionMar 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Phospholipase A2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0925
Polymers25,7402
Non-polymers3523
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-40 kcal/mol
Surface area11490 Å2
MethodPISA
2
A: Phospholipase A2
B: Phospholipase A2
hetero molecules

A: Phospholipase A2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,18510
Polymers51,4814
Non-polymers7046
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_775-y+2,-x+2,-z+1/21
Buried area4250 Å2
ΔGint-163 kcal/mol
Surface area22780 Å2
MethodPISA
3
A: Phospholipase A2
B: Phospholipase A2
hetero molecules

A: Phospholipase A2
B: Phospholipase A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,18510
Polymers51,4814
Non-polymers7046
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area4770 Å2
ΔGint-149 kcal/mol
Surface area22250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.656, 77.656, 68.424
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phospholipase A2 /


Mass: 13074.544 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja naja (Indian cobra) / Secretion: Venom / References: UniProt: P15445, phospholipase A2
#2: Protein Phospholipase A2 /


Mass: 12665.844 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Naja naja (Indian cobra) / Secretion: Venom / References: UniProt: P15445, phospholipase A2
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / 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 Å3/Da / Density % sol: 38.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10mM Sodium Cacodylate, 2mM Zinc acetate, 25% Ethanol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 278 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 14, 2002 / Details: Mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 100163 / Num. obs: 9636 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / Biso Wilson estimate: 51.3 Å2 / Rsym value: 0.113 / Net I/σ(I): 17.9
Reflection shellResolution: 2.3→2.34 Å / Mean I/σ(I) obs: 2.7 / Num. unique all: 404 / Rsym value: 0.229 / % possible all: 86.9

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LFJ

1lfj
PDB Unreleased entry


Resolution: 2.3→15 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 2405287.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 502 5.2 %RANDOM
Rwork0.225 ---
obs0.225 9636 99 %-
all-10138 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.6501 Å2 / ksol: 0.320318 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1780 0 17 242 2039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it2.981.5
X-RAY DIFFRACTIONc_mcangle_it4.682
X-RAY DIFFRACTIONc_scbond_it0.972
X-RAY DIFFRACTIONc_scangle_it1.572.5
LS refinement shellResolution: 2.3→2.34 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.392 90 6 %
Rwork0.34 1401 -
obs-404 94.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ACY.PARAMACY.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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