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- PDB-1bp1: CRYSTAL STRUCTURE OF BPI, THE HUMAN BACTERICIDAL PERMEABILITY-INC... -

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Basic information

Entry
Database: PDB / ID: 1bp1
TitleCRYSTAL STRUCTURE OF BPI, THE HUMAN BACTERICIDAL PERMEABILITY-INCREASING PROTEIN
ComponentsBACTERICIDAL/PERMEABILITY-INCREASING PROTEIN
KeywordsBACTERICIDAL / PERMEABILITY-INCREASING / LIPID-BINDING / LIPOPOLYSACCHARIDE-BINDING / ANTIBIOTIC
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
Lipid binding protein BPI/LBP / BPI/LBP/Plunc family / 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 ...Lipid binding protein BPI/LBP / BPI/LBP/Plunc family / 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 / MIRAS / Resolution: 2.4 Å
AuthorsBeamer, L.J. / Carroll, S.F. / Eisenberg, D.
Citation
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.
#1: Journal: Infect.Agents Dis. / Year: 1995
Title: Prospects for Use of Rbpi Fragments in the Treatment of Gram-Negative Bacterial Infections
Authors: Elsbach, P. / Weiss, J.
History
DepositionApr 8, 1997Processing site: BNL
Revision 1.0Sep 4, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 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
Revision 1.4Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
Water86548
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)185.600, 33.000, 85.200
Angle α, β, γ (deg.)90.00, 101.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 50703.691 Da / Num. of mol.: 1 / Mutation: S351A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: POLYMORPHONUCLEAR NEUTROPHILS
Cell line (production host): CHINESE HAMSTER OVARY CELLS (CHO)
Cellular location (production host): PRIMARY GRANULES / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P17213
#2: Chemical ChemComp-PC1 / 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE / 3-SN-PHOSPHATIDYLCHOLINE


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


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBPI HAS TWO SIMILAR DOMAINS WHICH SHOW NO SIGNIFICANT SEQUENCE SIMILARITY.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growpH: 6.8
Details: CRYSTALLIZED IN 12% PEG 8000, 0.2 M MG ACETATE, 0.1 NA CACODYLATE PH 6.8
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
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: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1994 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 18908 / % possible obs: 92.7 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 45 Å2 / Rsym value: 0.072
Reflection shellResolution: 2.4→2.5 Å / Mean I/σ(I) obs: 2.6 / % possible all: 94.5
Reflection
*PLUS
Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 94.5 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.4→50 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1926 10.2 %RANDOM
Rwork0.225 ---
obs0.225 18908 92.7 %-
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1--11.35 Å20 Å27.7 Å2
2--6.33 Å20 Å2
3---5.02 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3531 0 102 48 3681
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.24
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.771.5
X-RAY DIFFRACTIONx_mcangle_it32
X-RAY DIFFRACTIONx_scbond_it2.812
X-RAY DIFFRACTIONx_scangle_it4.532.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.455 275 8.7 %
Rwork0.368 2875 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.843 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.24
LS refinement shell
*PLUS
Rfactor obs: 0.368

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