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- PDB-1u4j: Crystal structure of a carbohydrate induced dimer of group I phos... -

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Basic information

Entry
Database: PDB / ID: 1u4j
TitleCrystal structure of a carbohydrate induced dimer of group I phospholipase A2 from Bungarus caeruleus at 2.1 A resolution
Componentsphospholipase A2 isoform 2
KeywordsHYDROLASE / Phospholipase A2 / Homodimer / Bungarus caeruleus / Mannose
Function / homology
Function and homology information


phospholipase A2 / phospholipase A2 activity / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / toxin activity / calcium ion binding / extracellular region
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETIC ACID / alpha-D-mannopyranose / Basic phospholipase A2 2
Similarity search - Component
Biological speciesBungarus caeruleus (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsSingh, G. / Gourinath, S. / Sharma, S. / Bhanumathi, S. / Betzel, C. / Srinivasan, A. / Singh, T.P.
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Crystal structure of a carbohydrate induced homodimer of phospholipase A(2) from Bungarus caeruleus at 2.1A resolution
Authors: Singh, G. / Gourinath, S. / Sarvanan, K. / Sharma, S. / Bhanumathi, S. / Betzel, C. / Yadav, S. / Srinivasan, A. / Singh, T.P.
History
DepositionJul 26, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 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

Downloads & links

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Assembly

Deposited unit
A: phospholipase A2 isoform 2
B: phospholipase A2 isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,61911
Polymers25,9612
Non-polymers6579
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-40 kcal/mol
Surface area11150 Å2
MethodPISA
2
A: phospholipase A2 isoform 2
hetero molecules

B: phospholipase A2 isoform 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,61911
Polymers25,9612
Non-polymers6579
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555-y+2/3,x-y+1/3,z+1/31
Buried area1810 Å2
ΔGint-44 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.360, 80.360, 99.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein phospholipase A2 isoform 2


Mass: 12980.627 Da / Num. of mol.: 2 / Fragment: residues 1-120 / Source method: isolated from a natural source / Source: (natural) Bungarus caeruleus (cobra) / References: UniProt: Q6SLM1, phospholipase A2
#5: Sugar ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 204 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.2 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 50mM Tris. HCl, 2.8M NaCl, 1mM NaN3, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 6, 2004 / Details: mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→14.3 Å / Num. all: 12541 / Num. obs: 12475 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.126 / Net I/σ(I): 6.4
Reflection shellResolution: 2.18→2.32 Å / Mean I/σ(I) obs: 2.1 / Rsym value: 0.24 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FE5

1fe5


Resolution: 2.18→14.26 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 48393.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Used weighted full matrix least squares procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.22 631 5.1 %RANDOM
Rwork0.194 ---
all0.202 12541 --
obs0.194 12397 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 76.7189 Å2 / ksol: 0.424515 e/Å3
Displacement parametersBiso mean: 24.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å21.77 Å20 Å2
2--0.16 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-4 Å
Luzzati sigma a0.19 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.18→14.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1796 0 28 209 2033
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 2.18→2.32 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 95 4.6 %
Rwork0.202 1952 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CARBOHYDRATE.PARAMCARBOHYDRATE.TOP
X-RAY DIFFRACTION5ACY.PARAMACY.TOP

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