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- PDB-1ijv: HUMAN BETA-DEFENSIN-1 -

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Basic information

Entry
Database: PDB / ID: 1ijv
TitleHUMAN BETA-DEFENSIN-1
ComponentsBeta-defensin 1
KeywordsDEFENSIN / HUMAN BETA-DEFENSIN-1 / BETA-DEFENSIN
Function / homology
Function and homology information


positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / 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 / microvesicle / CCR6 chemokine receptor binding / 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
BROMIDE ION / : / Beta-defensin 1
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.2 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: Atomic model / Version format compliance

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,59211
Polymers7,8812
Non-polymers7119
Water3,171176
1
A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,2765
Polymers3,9411
Non-polymers3364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,3156
Polymers3,9411
Non-polymers3755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.121, 47.243, 53.853
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Beta-defensin 1 / HBD-1


Mass: 3940.598 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / Source method: isolated from a natural source / Formula: H2O

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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: 1.75 Å3/Da / Density % sol: 29.8 % / Description: ANOMALOUS DATA USED FOR REFINEMENT
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium sulfate, sodium acetate, potassium bromide, glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.92021 / Wavelength: 0.92 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
10.920211
20.921
ReflectionResolution: 1.2→25 Å / Num. all: 87673 / Num. obs: 40500 / % possible obs: 96.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.033 / Net I/σ(I): 23.5
Reflection shellResolution: 1.2→1.24 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.227 / Mean I/σ(I) obs: 3 / % possible all: 86.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
SHARPphasing
DMmodel building
SHELXL-97refinement
SHELXphasing
DMphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.2→20 Å / Num. parameters: 7167 / Num. restraintsaints: 9055 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.193 76 1 %RANDOM
Rwork0.161 ---
all0.157 3966 --
obs0.161 3890 100 %-
Refine analyzeOccupancy sum hydrogen: 536 / Occupancy sum non hydrogen: 738
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms542 0 17 176 735
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.01
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.028
X-RAY DIFFRACTIONs_zero_chiral_vol0.07
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.08
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.03
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0.09

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