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- PDB-1bbc: STRUCTURE OF RECOMBINANT HUMAN RHEUMATOID ARTHRITIC SYNOVIAL FLUI... -

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Basic information

Entry
Database: PDB / ID: 1bbc
TitleSTRUCTURE OF RECOMBINANT HUMAN RHEUMATOID ARTHRITIC SYNOVIAL FLUID PHOSPHOLIPASE A2 AT 2.2 ANGSTROMS RESOLUTION
ComponentsPHOSPHOLIPASE A2
KeywordsHYDROLASE / CARBOXYLIC ESTER HYDROLASE
Function / homology
Function and homology information


regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / intestinal stem cell homeostasis ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / intestinal stem cell homeostasis / phosphatidylglycerol metabolic process / phospholipase A2 activity / phosphatidylcholine metabolic process / phospholipase A2 / low-density lipoprotein particle remodeling / positive regulation of macrophage derived foam cell differentiation / calcium-dependent phospholipase A2 activity / Antimicrobial peptides / arachidonate secretion / lipid catabolic process / negative regulation of T cell proliferation / phospholipid metabolic process / secretory granule / angiotensin-activated signaling pathway / phospholipid binding / positive regulation of inflammatory response / killing of cells of another organism / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / 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 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phospholipase A2, membrane associated
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsWery, J.-P. / Schevitz, R.W. / Clawson, D.K. / Bobbitt, J.L. / Dow, E.R. / Gamboa, G. / Goodsonjunior, T. / Hermann, R.B. / Kramer, R.M. / Mcclure, D.B. ...Wery, J.-P. / Schevitz, R.W. / Clawson, D.K. / Bobbitt, J.L. / Dow, E.R. / Gamboa, G. / Goodsonjunior, T. / Hermann, R.B. / Kramer, R.M. / Mcclure, D.B. / Mihelich, E.D. / Putnam, J.E. / Sharp, J.D. / Stark, D.H. / Teater, C. / Warrick, M.W. / Jones, N.D.
Citation
Journal: Nature / Year: 1991
Title: Structure of recombinant human rheumatoid arthritic synovial fluid phospholipase A2 at 2.2 A resolution.
Authors: Wery, J.P. / Schevitz, R.W. / Clawson, D.K. / Bobbitt, J.L. / Dow, E.R. / Gamboa, G. / Goodson Jr., T. / Hermann, R.B. / Kramer, R.M. / McClure, D.B. / Mihelich, E.D. / Putnam, J.E. / Sharp, ...Authors: Wery, J.P. / Schevitz, R.W. / Clawson, D.K. / Bobbitt, J.L. / Dow, E.R. / Gamboa, G. / Goodson Jr., T. / Hermann, R.B. / Kramer, R.M. / McClure, D.B. / Mihelich, E.D. / Putnam, J.E. / Sharp, J.D. / Stark, D.H. / Teater, C. / Warrick, M.W. / Jones, N.D.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Structure and Properties of a Human Non-Pancreatic Phospholipase A2
Authors: Kramer, R.M. / Hession, C. / Johansen, B. / Hayes, G. / Mcgray, P. / Chow, E.P. / Tizard, R. / Pepinsky, R.B.
History
DepositionMay 4, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 29, 2012Group: Database references
Revision 1.4Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.5Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.6Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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


Theoretical massNumber of molelcules
Total (without water)13,9451
Polymers13,9451
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.610, 54.560, 31.320
Angle α, β, γ (deg.)90.00, 97.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOLIPASE A2


Mass: 13945.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P14555, phospholipase A2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.98 %
Crystal grow
*PLUS
pH: 5.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110.0 mg/mlprotein11
2100 mMcitrate11
34.0 Mammonium chloride11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Rmerge(I) obs: 0.063

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.178 -
obs0.178 4114
Refinement stepCycle: LAST / Resolution: 2.2→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 0 87 1053
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.6362
X-RAY DIFFRACTIONx_mcangle_it2.5552.5
X-RAY DIFFRACTIONx_scbond_it2.6572.5
X-RAY DIFFRACTIONx_scangle_it3.8353.5
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 6 Å / Num. reflection all: 4114 / σ(F): 0 / Rfactor all: 0.178
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.030.036
X-RAY DIFFRACTIONx_planar_d0.040.04
X-RAY DIFFRACTIONx_plane_restr0.0250.016
X-RAY DIFFRACTIONx_chiral_restr0.130.158

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