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- PDB-1ewf: THE 1.7 ANGSTROM CRYSTAL STRUCTURE OF BPI -

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Basic information

Entry
Database: PDB / ID: 1ewf
TitleTHE 1.7 ANGSTROM CRYSTAL STRUCTURE OF BPI
ComponentsBACTERICIDAL/PERMEABILITY-INCREASING PROTEIN
KeywordsANTIBIOTIC / BACTERICIDAL / PERMEABILITY-INCREASING / LIPID-BINDING / LIPOPOLYSACCHARIDE-BINDING
Function / homology
Function and homology information


negative regulation of macrophage activation / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of interleukin-8 production / Antimicrobial peptides / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / lipopolysaccharide-mediated signaling pathway / lipopolysaccharide binding / specific granule lumen / azurophil granule lumen ...negative regulation of macrophage activation / Toll Like Receptor 4 (TLR4) Cascade / negative regulation of interleukin-8 production / Antimicrobial peptides / negative regulation of interleukin-6 production / negative regulation of tumor necrosis factor production / lipopolysaccharide-mediated signaling pathway / lipopolysaccharide binding / specific granule lumen / azurophil granule lumen / defense response to Gram-negative bacterium / innate immune response / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane
Similarity search - Function
BPI/LBP/Plunc family / Lipid binding protein BPI/LBP / Bactericidal permeability-increasing protein; domain 2 / Bactericidal permeability-increasing protein; domain 2 / Lipid-binding serum glycoprotein, C-terminal / Lipid-binding serum glycoprotein, conserved site / LBP / BPI / CETP family, C-terminal domain / LBP / BPI / CETP family signature. / BPI/LBP/CETP N-terminal domain / BPI/LBP/CETP C-terminal domain ...BPI/LBP/Plunc family / Lipid binding protein BPI/LBP / Bactericidal permeability-increasing protein; domain 2 / Bactericidal permeability-increasing protein; domain 2 / Lipid-binding serum glycoprotein, C-terminal / Lipid-binding serum glycoprotein, conserved site / LBP / BPI / CETP family, C-terminal domain / LBP / BPI / CETP family signature. / BPI/LBP/CETP N-terminal domain / BPI/LBP/CETP C-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Lipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / Bactericidal permeability-increasing protein; domain 1 / Super Roll / Alpha Beta
Similarity search - Domain/homology
1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Bactericidal permeability-increasing protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKleiger, G. / Beamer, L.J. / Grothe, R. / Mallick, P. / Eisenberg, D.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: The 1.7 A crystal structure of BPI: a study of how two dissimilar amino acid sequences can adopt the same fold.
Authors: Kleiger, G. / Beamer, L.J. / Grothe, R. / Mallick, P. / Eisenberg, D.
#1: Journal: Science / Year: 1997
Title: Crystal Structure of Human BPI and Two Bound Phospholipids at 2.4 Angstrom Resolution
Authors: Beamer, L.J. / Carroll, S.F. / Eisenberg, D.
History
DepositionApr 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Database references
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow
Item: _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2843
Polymers50,7041
Non-polymers1,5802
Water6,972387
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)184.320, 31.230, 80.660
Angle α, β, γ (deg.)90.00, 103.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BACTERICIDAL/PERMEABILITY-INCREASING PROTEIN / BPI


Mass: 50703.625 Da / Num. of mol.: 1 / Mutation: S351A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Description: MAMMALIAN CHO CELLS USED FOR RECOMBINANT EXPRESSION OF THE PROTEIN
Cell (production host): OVARY CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P17213
#2: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE / Phosphatidylcholine


Mass: 790.145 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H88NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA NATURALLY OCCURRING POLYMORPHISM EXISTS AT RESIDUE 185 FOR HUMAN BPI. THE CLONE USED FOR ...A NATURALLY OCCURRING POLYMORPHISM EXISTS AT RESIDUE 185 FOR HUMAN BPI. THE CLONE USED FOR EXPRESSION OF BPI HAS GLU AT THIS POSITION, ALTHOUGH THE CLONE FOR THE SWISSPROT ENTRY HAS LYS AT THE SAME POSITION.

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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: 44.78 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 12 % PEG 6000, 0.2 M Mg Acetate, 0.1 M Na Cacodylate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 16K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18.5 mg/mlprotein1drop
212 %(w/v)PEG80001reservoir
3200 mMmagnesium acetate1reservoir
4100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.975
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 6, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 47198 / Num. obs: 47198 / % possible obs: 94.2 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 24 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.201 / Num. unique all: 3300 / % possible all: 67
Reflection shell
*PLUS
% possible obs: 67 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementResolution: 1.7→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.25 4755 -random selection of 10 percent of all data
Rwork0.198 ---
all-50128 --
obs-47197 94.2 %-
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3521 0 97 387 4005
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.017
X-RAY DIFFRACTIONc_angle_deg2
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.33

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