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- PDB-1c1j: STRUCTURE OF CADMIUM-SUBSTITUTED PHOSPHOLIPASE A2 FROM AGKISTROND... -

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Basic information

Entry
Database: PDB / ID: 1c1j
TitleSTRUCTURE OF CADMIUM-SUBSTITUTED PHOSPHOLIPASE A2 FROM AGKISTRONDON HALYS PALLAS AT 2.8 ANGSTROMS RESOLUTION
ComponentsBASIC PHOSPHOLIPASE A2
KeywordsHYDROLASE / VENOM / PHOSPHOLIPASE A2 / CADMIUM / CATALYTIC MECHANISM
Function / homology
Function and homology information


phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / fatty acid biosynthetic process ...phospholipase A2 activity => GO:0004623 / phospholipase A2 activity => GO:0004623 / phospholipase A2 activity / calcium-dependent phospholipase A2 activity / phospholipase A2 / arachidonate secretion / phospholipid metabolic process / lipid catabolic process / phospholipid binding / fatty acid biosynthetic process / positive regulation of fibroblast proliferation / toxin activity / signaling receptor binding / 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
: / Basic phospholipase A2 B / Basic phospholipase A2
Similarity search - Component
Biological speciesGloydius halys (Halys viper)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsZhang, H.-l. / Zhang, Y.-q. / Song, S.-y. / Zhou, Y. / Lin, Z.-j.
Citation
Journal: Protein Pept.Lett. / Year: 1999
Title: Structure of Cadmium-substituted Phospholipase A2 from Agkistrodon halys Pallas at 2.8 Angstroms Resolution
Authors: Zhang, H.-l. / Zhang, Y.-q. / Song, S.-y. / Zhou, Y. / Lin, Z.-j.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: Structure of a Basic Phospholipase A2 from Agkistrodon halys Pallas at 2.13 Angstroms Resolution
Authors: Zhao, K. / Song, S. / Lin, Z. / Zhou, Y.
History
DepositionJul 22, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BASIC PHOSPHOLIPASE A2
B: BASIC PHOSPHOLIPASE A2
C: BASIC PHOSPHOLIPASE A2
D: BASIC PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,94812
Polymers55,6894
Non-polymers1,2598
Water84747
1
A: BASIC PHOSPHOLIPASE A2
D: BASIC PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5867
Polymers27,8442
Non-polymers7425
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BASIC PHOSPHOLIPASE A2
C: BASIC PHOSPHOLIPASE A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3625
Polymers27,8442
Non-polymers5173
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.180, 54.010, 108.490
Angle α, β, γ (deg.)90.00, 111.59, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
BASIC PHOSPHOLIPASE A2 / E.C.3.1.1.4 / PA2-I / PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE


Mass: 13922.184 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Gloydius halys (Halys viper)
References: UniProt: P04417, UniProt: O42187*PLUS, phospholipase A2
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, n-octyl beta-D-glycopyranoside, CaCl2, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K

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Data collection

DiffractionMean temperature: 280 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Mar 17, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 13527 / Num. obs: 13017 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 11.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.37 / Num. unique all: 1247 / % possible all: 95

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR3.851refinement
RefinementResolution: 2.8→8 Å / Cross valid method: THROUGHOUT / σ(F): 2
Details: Used 2-fold noncrystallographic symmetry (NCS) restraints
RfactorNum. reflection% reflectionSelection details
Rfree0.282 1102 10 %RANDOM
Rwork0.201 ---
all-11762 --
obs-11066 95.3 %-
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3856 0 46 47 3949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_deg1.23
X-RAY DIFFRACTIONx_dihedral_angle_d26.45
X-RAY DIFFRACTIONx_improper_angle_d0.55

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