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- PDB-2nle: Human beta-defensin-1 (Mutant Gln11Ala) -

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Basic information

Entry
Database: PDB / ID: 2nle
TitleHuman beta-defensin-1 (Mutant Gln11Ala)
ComponentsBeta-defensin 1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / chemotactic / defensin / mutant
Function / homology
Function and homology information


positive regulation of flagellated sperm motility involved in capacitation / CCR6 chemokine receptor binding / microvesicle / Beta defensins / Defensins / sperm midpiece / innate immune response in mucosa / response to bacterium / calcium-mediated signaling / Golgi lumen ...positive regulation of flagellated sperm motility involved in capacitation / CCR6 chemokine receptor binding / microvesicle / Beta defensins / Defensins / sperm midpiece / innate immune response in mucosa / response to bacterium / calcium-mediated signaling / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / innate immune response / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane
Similarity search - Function
Beta defensin type / Beta defensin
Similarity search - Domain/homology
ACETATE ION / Beta-defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsLubkowski, J. / Pazgier, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Studies of the Biological Properties of Human beta-Defensin 1.
Authors: Pazgier, M. / Prahl, A. / Hoover, D.M. / Lubkowski, J.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-defensin 1
B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1446
Polymers7,7972
Non-polymers3474
Water2,360131
1
A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2465
Polymers3,8991
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)3,8991
Polymers3,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.220, 22.780, 40.150
Angle α, β, γ (deg.)90.00, 108.50, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer

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Components

#1: Protein/peptide Beta-defensin 1 / BD-1 / Defensin / beta 1 / hBD-1


Mass: 3898.518 Da / Num. of mol.: 2 / Fragment: human beta-defensin 1, residues 33-68 / Mutation: L13A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFB1, BD1, HBD1 / Plasmid: pAED4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: P60022
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 1.9 Å3/Da / Density % sol: 35.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: PEG 4000, AMMONIUM SULFATE, SODIUM ACETATE, GLYCEROL, pH 4.6, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.9718 / Wavelength: 0.9718 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 18, 2005
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9718 Å / Relative weight: 1
ReflectionResolution: 1.35→40 Å / Num. all: 13193 / Num. obs: 13193 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.037 / Χ2: 1.099 / Net I/σ(I): 29
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 7.5 / Num. unique all: 1284 / Χ2: 2.257 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IJV

1ijv


Resolution: 1.35→30 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.047 / SU ML: 0.039 / SU R Cruickshank DPI: 0.071 / Cross valid method: THROUGHOUT / ESU R Free: 0.065 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.198 926 7 %RANDOM
Rwork0.151 ---
all0.154 13183 --
obs0.154 13183 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.479 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0.08 Å2
2---0.29 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.35→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms541 0 19 135 695
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0185720.022
X-RAY DIFFRACTIONr_angle_refined_deg1.8627701.972
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.423705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1912023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.5629515
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.165215
X-RAY DIFFRACTIONr_chiral_restr0.139760.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0084160.02
X-RAY DIFFRACTIONr_nbd_refined0.2342610.2
X-RAY DIFFRACTIONr_nbtor_refined0.3063960.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1531020.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.212720.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.156350.2
X-RAY DIFFRACTIONr_mcbond_it2.0513711.5
X-RAY DIFFRACTIONr_mcangle_it2.7445672
X-RAY DIFFRACTIONr_scbond_it4.1962383
X-RAY DIFFRACTIONr_scangle_it4.8682034.5
X-RAY DIFFRACTIONRIGID-BOND RESTRAINTS (A**2)3.5526093
X-RAY DIFFRACTIONSPHERICITY; FREE ATOMS (A**2)1356.701
X-RAY DIFFRACTIONSPHERICITY; BONDED ATOMS (A**2)5605.401
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 63 -
Rwork0.183 890 -
obs-953 99.48 %

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