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- PDB-1fd4: HUMAN BETA-DEFENSIN 2 -

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Basic information

Entry
Database: PDB / ID: 1fd4
TitleHUMAN BETA-DEFENSIN 2
ComponentsBETA-DEFENSIN 2
KeywordsANTIMICROBIAL PEPTIDE / DEFENSIN / HUMAN BETA-DEFENSIN 2 / BETA-DEFENSIN
Function / homology
Function and homology information


CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis ...CCR6 chemokine receptor binding / Beta defensins / Defensins / antifungal innate immune response / chemoattractant activity / defense response to fungus / phosphatidylinositol-4,5-bisphosphate binding / cell chemotaxis / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / immune response / G protein-coupled receptor signaling pathway / extracellular space / extracellular region
Similarity search - Function
Antimicrobial Peptide, Beta-defensin 2; Chain A / Antimicrobial Peptide, Beta-defensin 2; Chain A / Beta defensin type / Beta defensin / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family / Roll / Alpha Beta
Similarity search - Domain/homology
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsHoover, D.M. / Lubkowski, J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: The structure of human beta-defensin-2 shows evidence of higher order oligomerization.
Authors: Hoover, D.M. / Rajashankar, K.R. / Blumenthal, R. / Puri, A. / Oppenheim, J.J. / Chertov, O. / Lubkowski, J.
History
DepositionJul 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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Assembly

Deposited unit
A: BETA-DEFENSIN 2
B: BETA-DEFENSIN 2
C: BETA-DEFENSIN 2
D: BETA-DEFENSIN 2
E: BETA-DEFENSIN 2
F: BETA-DEFENSIN 2
G: BETA-DEFENSIN 2
H: BETA-DEFENSIN 2
I: BETA-DEFENSIN 2
J: BETA-DEFENSIN 2
K: BETA-DEFENSIN 2
L: BETA-DEFENSIN 2
M: BETA-DEFENSIN 2
N: BETA-DEFENSIN 2
O: BETA-DEFENSIN 2
P: BETA-DEFENSIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,95721
Polymers69,47616
Non-polymers4805
Water14,520806
1
A: BETA-DEFENSIN 2
B: BETA-DEFENSIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7813
Polymers8,6852
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-30 kcal/mol
Surface area4830 Å2
MethodPISA
2
C: BETA-DEFENSIN 2
D: BETA-DEFENSIN 2


Theoretical massNumber of molelcules
Total (without water)8,6852
Polymers8,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1010 Å2
ΔGint-13 kcal/mol
Surface area4890 Å2
MethodPISA
3
E: BETA-DEFENSIN 2
F: BETA-DEFENSIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7813
Polymers8,6852
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-24 kcal/mol
Surface area4650 Å2
MethodPISA
4
G: BETA-DEFENSIN 2
H: BETA-DEFENSIN 2


Theoretical massNumber of molelcules
Total (without water)8,6852
Polymers8,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-11 kcal/mol
Surface area4770 Å2
MethodPISA
5
I: BETA-DEFENSIN 2
J: BETA-DEFENSIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,8774
Polymers8,6852
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-11 kcal/mol
Surface area4710 Å2
MethodPISA
6
K: BETA-DEFENSIN 2
L: BETA-DEFENSIN 2


Theoretical massNumber of molelcules
Total (without water)8,6852
Polymers8,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1000 Å2
ΔGint-13 kcal/mol
Surface area5090 Å2
MethodPISA
7
M: BETA-DEFENSIN 2
N: BETA-DEFENSIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,7813
Polymers8,6852
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-38 kcal/mol
Surface area4860 Å2
MethodPISA
8
O: BETA-DEFENSIN 2
P: BETA-DEFENSIN 2


Theoretical massNumber of molelcules
Total (without water)8,6852
Polymers8,6852
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-12 kcal/mol
Surface area4930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.525, 79.950, 74.271
Angle α, β, γ (deg.)90.00, 105.30, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer.

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Components

#1: Protein/peptide
BETA-DEFENSIN 2 / HBD-2 / SKIN-ANTIMICROBIAL PEPTIDE 1


Mass: 4342.271 Da / Num. of mol.: 16 / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS)
References: UniProt: O15263
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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 Å3/Da / Density % sol: 45.21 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 4000, tris, lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.15K
Crystal grow
*PLUS
Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 %PEG40001reservoir
20.066 MTris-HCl1reservoir
30.133 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.979
DetectorType: ADSC / Detector: CCD / Date: Oct 2, 1999 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 65644 / Num. obs: 65644 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 10.2 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 24.2
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 4.7 / % possible all: 96.3
Reflection
*PLUS
% possible obs: 97.1 % / Num. measured all: 165583
Reflection shell
*PLUS
% possible obs: 96.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN BETA-DEFESIN-2

Resolution: 1.7→30 Å / Num. parameters: 2327 / Num. restraintsaints: 2138 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 6512 11 %RANDOM
Rwork0.1878 ---
all0.1876 57662 --
obs0.1876 57662 85.4 %-
Refine analyzeNum. disordered residues: 3 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5615
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4979 0 25 814 5818
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.444
X-RAY DIFFRACTIONs_zero_chiral_vol0.03
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.01
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 11 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.006
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_plane_restr0.444
X-RAY DIFFRACTIONs_chiral_restr0.03

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