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- PDB-1iju: HUMAN BETA-DEFENSIN-1 -

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Basic information

Entry
Database: PDB / ID: 1iju
TitleHUMAN BETA-DEFENSIN-1
ComponentsBETA-DEFENSIN 1
KeywordsANTIBIOTIC / DEFENSIN / HUMAN BETA-DEFENSIN-1 / BETA-DEFENSIN
Function / homology
Function and homology information


positive regulation of flagellated sperm motility involved in capacitation / CCR6 chemokine receptor binding / microvesicle / Beta defensins / Defensins / innate immune response in mucosa / response to bacterium / calcium-mediated signaling / Golgi lumen / chemotaxis ...positive regulation of flagellated sperm motility involved in capacitation / CCR6 chemokine receptor binding / microvesicle / Beta defensins / Defensins / innate immune response in mucosa / response to bacterium / calcium-mediated signaling / Golgi lumen / chemotaxis / sperm midpiece / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / defense response to Gram-negative bacterium / defense response to bacterium / defense response to Gram-positive 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
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsHoover, D.M. / Lubkowski, J.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The structure of human beta-defensin-1: new insights into structural properties of beta-defensins.
Authors: Hoover, D.M. / Chertov, O. / Lubkowski, J.
History
DepositionApr 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Apr 3, 2024Group: 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 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: BETA-DEFENSIN 1
B: BETA-DEFENSIN 1
C: BETA-DEFENSIN 1
D: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,61913
Polymers15,7624
Non-polymers8579
Water4,882271
1
A: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1293
Polymers3,9411
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1333
Polymers3,9411
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2254
Polymers3,9411
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1333
Polymers3,9411
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: BETA-DEFENSIN 1
D: BETA-DEFENSIN 1
hetero molecules

A: BETA-DEFENSIN 1
B: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,61913
Polymers15,7624
Non-polymers8579
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3780 Å2
ΔGint-127 kcal/mol
Surface area9150 Å2
MethodPISA
6
C: BETA-DEFENSIN 1
D: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,3587
Polymers7,8812
Non-polymers4765
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-54 kcal/mol
Surface area4950 Å2
MethodPISA
7
A: BETA-DEFENSIN 1
B: BETA-DEFENSIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2616
Polymers7,8812
Non-polymers3804
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-56 kcal/mol
Surface area5020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.817, 26.814, 58.833
Angle α, β, γ (deg.)90.00, 102.13, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
BETA-DEFENSIN 1 / HBD-1


Mass: 3940.598 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS).
References: UniProt: P60022
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 1.77 Å3/Da / Density % sol: 30.4 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium sulfate, sodium acetate, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
230 %PEG40001reservoir
315 %glycerol1reservoir
40.1 Mammonium sulfate1reservoir
50.1 M1reservoirNaOAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.98 / Wavelength: 0.979 Å
DetectorType: ADSC / Detector: CCD / Date: Mar 4, 2001 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.9791
ReflectionResolution: 1.4→20 Å / Num. all: 87587 / Num. obs: 26325 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 27.2
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 2.5 / % possible all: 64.1
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 87587
Reflection shell
*PLUS
% possible obs: 64.1 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN BETA-DEFENSIN-1

Resolution: 1.4→20 Å / Num. parameters: 6199 / Num. restraintsaints: 5551 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.217 111 4 %RANDOM
Rwork0.168 ---
all0.175 25193 --
obs0.168 2408 92.1 %-
Refine analyzeNum. disordered residues: 1 / Occupancy sum hydrogen: 1040 / Occupancy sum non hydrogen: 1350
Refinement stepCycle: LAST / Resolution: 1.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 47 271 1402
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.08
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 4.4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_plane_restr0.028

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