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- PDB-6baq: Mus musculus BPIFA1 -

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Basic information

Entry
Database: PDB / ID: 6baq
TitleMus musculus BPIFA1
ComponentsBPI fold-containing family A member 1
KeywordsANTIMICROBIAL PROTEIN / lung defense protein / surfactant protein / lipid binding protein
Function / homology
Function and homology information


Antimicrobial peptides / immune response in nasopharyngeal-associated lymphoid tissue / negative regulation of single-species biofilm formation in or on host organism / regulation of sodium ion transmembrane transport / multicellular organismal-level water homeostasis / surfactant homeostasis / microvillus / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / innate immune response ...Antimicrobial peptides / immune response in nasopharyngeal-associated lymphoid tissue / negative regulation of single-species biofilm formation in or on host organism / regulation of sodium ion transmembrane transport / multicellular organismal-level water homeostasis / surfactant homeostasis / microvillus / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / innate immune response / lipid binding / extracellular space / extracellular region
Similarity search - Function
: / 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
BPI fold-containing family A member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.50260996677 Å
AuthorsLittle, M.S. / Redinbo, M.R.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2018
Title: Crystal structure of the mouse innate immunity factor bacterial permeability-increasing family member A1.
Authors: Little, M.S. / Redinbo, M.R.
History
DepositionOct 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Apr 24, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_id / _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_asym_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 / _struct_conn.ptnr2_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BPI fold-containing family A member 1
B: BPI fold-containing family A member 1
C: BPI fold-containing family A member 1
D: BPI fold-containing family A member 1
E: BPI fold-containing family A member 1
F: BPI fold-containing family A member 1
G: BPI fold-containing family A member 1
H: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,64176
Polymers201,7898
Non-polymers1,85268
Water5,855325
1
A: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,47612
Polymers25,2241
Non-polymers25311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3978
Polymers25,2241
Non-polymers1737
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,50010
Polymers25,2241
Non-polymers2769
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3165
Polymers25,2241
Non-polymers924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,43010
Polymers25,2241
Non-polymers2079
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3396
Polymers25,2241
Non-polymers1155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,61515
Polymers25,2241
Non-polymers39114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: BPI fold-containing family A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,56910
Polymers25,2241
Non-polymers3459
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)132.200, 200.582, 89.499
Angle α, β, γ (deg.)90.000, 126.150, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUILEILE(chain 'A' and ((resid 70 and (name N or name...AA72 - 10238 - 68
12LEULEUPROPRO(chain 'A' and ((resid 70 and (name N or name...AA126 - 16992 - 135
13GLYGLYASNASN(chain 'A' and ((resid 70 and (name N or name...AA172 - 217138 - 183
14THRTHRILEILE(chain 'A' and ((resid 70 and (name N or name...AA220 - 276186 - 242
21LEULEUILEILE(chain 'B' and ((resid 70 and (name N or name...BB72 - 10238 - 68
22LEULEUPROPRO(chain 'B' and ((resid 70 and (name N or name...BB126 - 16992 - 135
23GLYGLYASNASN(chain 'B' and ((resid 70 and (name N or name...BB172 - 217138 - 183
24THRTHRILEILE(chain 'B' and ((resid 70 and (name N or name...BB220 - 276186 - 242
31LEULEUILEILE(chain 'C' and ((resid 70 and (name N or name...CC72 - 10238 - 68
32LEULEUPROPRO(chain 'C' and ((resid 70 and (name N or name...CC126 - 16992 - 135
33GLYGLYASNASN(chain 'C' and ((resid 70 and (name N or name...CC172 - 217138 - 183
34THRTHRILEILE(chain 'C' and ((resid 70 and (name N or name...CC220 - 276186 - 242
41LEULEUILEILE(chain 'D' and ((resid 70 and (name N or name...DD72 - 10238 - 68
42LEULEUPROPRO(chain 'D' and ((resid 70 and (name N or name...DD126 - 16992 - 135
43GLYGLYASNASN(chain 'D' and ((resid 70 and (name N or name...DD172 - 217138 - 183
44THRTHRILEILE(chain 'D' and ((resid 70 and (name N or name...DD220 - 276186 - 242
51LEULEUILEILE(chain 'E' and ((resid 70 and (name N or name...EE72 - 10238 - 68
52LEULEUPROPRO(chain 'E' and ((resid 70 and (name N or name...EE126 - 16992 - 135
53GLYGLYASNASN(chain 'E' and ((resid 70 and (name N or name...EE172 - 217138 - 183
54THRTHRILEILE(chain 'E' and ((resid 70 and (name N or name...EE220 - 276186 - 242
61LEULEUILEILE(chain 'F' and ((resid 70 and (name N or name...FF72 - 10238 - 68
62LEULEUPROPRO(chain 'F' and ((resid 70 and (name N or name...FF126 - 16992 - 135
63GLYGLYASNASN(chain 'F' and ((resid 70 and (name N or name...FF172 - 217138 - 183
64THRTHRILEILE(chain 'F' and ((resid 70 and (name N or name...FF220 - 276186 - 242
71LEULEUILEILE(chain 'G' and ((resid 70 and (name N or name...GG72 - 10238 - 68
72LEULEUPROPRO(chain 'G' and ((resid 70 and (name N or name...GG126 - 16992 - 135
73GLYGLYASNASN(chain 'G' and ((resid 70 and (name N or name...GG172 - 217138 - 183
74THRTHRILEILE(chain 'G' and ((resid 70 and (name N or name...GG220 - 276186 - 242
81LEULEUILEILE(chain 'H' and (resid 70 or resid 72 through 94...HH72 - 10238 - 68
82LEULEUPROPRO(chain 'H' and (resid 70 or resid 72 through 94...HH126 - 16992 - 135
83GLYGLYASNASN(chain 'H' and (resid 70 or resid 72 through 94...HH172 - 217138 - 183
84THRTHRILEILE(chain 'H' and (resid 70 or resid 72 through 94...HH220 - 276186 - 242

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Components

#1: Protein
BPI fold-containing family A member 1 / Palate lung and nasal epithelium clone protein


Mass: 25223.580 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Bpifa1, Plunc, Splunc1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P97361
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 63 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.19 %
Crystal growTemperature: 310.15 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 20% PEG 1000, 0.2 M Lithium Sulfate, 0.1 M Phosphate-citrate pH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.5→41.8 Å / Num. obs: 64175 / % possible obs: 98.86 % / Redundancy: 6 % / Biso Wilson estimate: 32.4327951628 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 24.8

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Processing

Software
NameVersionClassification
Coot1.12_2829refinement
PHENIX1.12_2829refinement
PHENIXmodel building
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KGH

4kgh


Resolution: 2.50260996677→41.7889790055 Å / SU ML: 0.352170988553 / Cross valid method: FREE R-VALUE / σ(F): 1.35927248893 / Phase error: 34.392262867
RfactorNum. reflection% reflection
Rfree0.27823603791 1992 3.11927467468 %
Rwork0.221085685215 --
obs0.222884893344 63861 98.8361475245 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 39.4376978181 Å2
Refinement stepCycle: LAST / Resolution: 2.50260996677→41.7889790055 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11049 0 88 325 11462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0080723298231111229
X-RAY DIFFRACTIONf_angle_d1.1457828333315372
X-RAY DIFFRACTIONf_chiral_restr0.06527316605582051
X-RAY DIFFRACTIONf_plane_restr0.008885357942781932
X-RAY DIFFRACTIONf_dihedral_angle_d5.543466392926994
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5026-2.56520.3416761859571330.2783505255324112X-RAY DIFFRACTION92.5239755885
2.5652-2.63450.3419609733521430.2550430978234437X-RAY DIFFRACTION99.1986138185
2.6345-2.7120.2891608505511420.2461489691054429X-RAY DIFFRACTION99.5643650621
2.712-2.79960.3348581771091430.2402927523874464X-RAY DIFFRACTION99.7402035073
2.7996-2.89960.319994876541430.2474657325364420X-RAY DIFFRACTION99.8249835922
2.8996-3.01570.2830076298981430.2431804575114472X-RAY DIFFRACTION99.8269521955
3.0157-3.15290.3174806876681430.2379389887694454X-RAY DIFFRACTION99.7612847222
3.1529-3.3190.2867884970651440.225467676284470X-RAY DIFFRACTION99.8485176369
3.319-3.52690.2828199666921420.2252509124174465X-RAY DIFFRACTION99.9132509217
3.5269-3.7990.274578709891440.2200755289244444X-RAY DIFFRACTION99.9128919861
3.799-4.1810.2676064614731440.1994417170764479X-RAY DIFFRACTION99.9783737024
4.181-4.78530.2221118226831440.1756804694654481X-RAY DIFFRACTION99.8704383502
4.7853-6.0260.2465665047471440.2123232737244490X-RAY DIFFRACTION99.6987951807
6.026-41.79480.2673971194591400.2171657003414252X-RAY DIFFRACTION94.087403599

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