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- PDB-5ki9: Crystal structure of human beta-defensin 4 (HBD4) -

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Basic information

Entry
Database: PDB / ID: 5ki9
TitleCrystal structure of human beta-defensin 4 (HBD4)
ComponentsBeta-defensin 104
KeywordsANTIMICROBIAL PROTEIN / DEFENSIN / ANTIMICROBIAL / CHEMOTACTIC / DIMERIZATION
Function / homology
Function and homology information


Beta defensins / Defensins / cellular response to phorbol 13-acetate 12-myristate / positive chemotaxis / chemoattractant activity / monocyte chemotaxis / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / innate immune response / extracellular region
Similarity search - Function
Beta-defensin / Beta defensin
Similarity search - Domain/homology
trifluoroacetic acid / Beta-defensin 104
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å
AuthorsJacek, L. / Adam, P. / Marzenam, P.
CitationJournal: To Be Published
Title: Human beta-Defensin 4: defensin without the "twist"
Authors: Adam, P. / Marzenam, P. / Jerry, A. / Jacek, L.
History
DepositionJun 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 2, 2025Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Beta-defensin 104
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6595
Polymers5,2571
Non-polymers4024
Water30617
1
A: Beta-defensin 104
hetero molecules

A: Beta-defensin 104
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,31910
Polymers10,5142
Non-polymers8048
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3070 Å2
ΔGint-92 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.704, 41.704, 52.945
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Detailsauthor states the biological assembly is unknown

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Components

#1: Protein/peptide Beta-defensin 104 / Beta-defensin 4 / hBD-4 / Defensin / beta 104


Mass: 5257.094 Da / Num. of mol.: 1 / Fragment: UNP residues 23-65
Source method: isolated from a genetically manipulated source
Details: LYSINE RESIDUES ARE DI-METHYLATED / Source: (gene. exp.) Homo sapiens (human) / Gene: DEFB104A, DEFB104, DEFB4, DEFB104B / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WTQ1
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-TFA / trifluoroacetic acid


Mass: 114.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2HF3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.19 Å3/Da / Density % sol: 43.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25.5% PEG 8,000, 0.085 M sodium acetate buffer pH 4.5, 0.17 M Lithium Sulfate, 15% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 6994 / % possible obs: 95.6 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.014 / Rrim(I) all: 0.06 / Χ2: 1.697 / Net I/av σ(I): 90.17 / Net I/σ(I): 16.7 / Num. measured all: 116371
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.55-1.587.30.86518
1.58-1.6111.70.7031100
1.61-1.6412.40.5091100
1.64-1.6712.20.4261100
1.67-1.7112.60.3191100
1.71-1.7512.20.2741100
1.75-1.7912.50.1971100
1.79-1.8412.30.151100
1.84-1.8912.40.1191100
1.89-1.9512.40.0941100
1.95-2.0212.30.0831100
2.02-2.112.20.071100
2.1-2.216.60.1771100
2.2-2.3225.80.21100
2.32-2.4625.80.1351100
2.46-2.6525.60.1131100
2.65-2.9225.20.0881100
2.92-3.3423.90.0621100
3.34-4.2121.60.0491100
4.21-5015.60.0411100

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
SHELXphasing
REFMAC5.5.0104refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MAD / Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.658 / SU ML: 0.087 / SU R Cruickshank DPI: 0.1588 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2678 645 9.8 %RANDOM
Rwork0.23 ---
obs0.2336 5916 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 170.24 Å2 / Biso mean: 51.173 Å2 / Biso min: 30.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.99 Å2
Refinement stepCycle: final / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms363 0 21 17 401
Biso mean--56.03 74.82 -
Num. residues----43
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021389
X-RAY DIFFRACTIONr_angle_refined_deg2.052.047523
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.294542
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.16120.520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.2581557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.028157
X-RAY DIFFRACTIONr_chiral_restr0.1290.246
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02292
X-RAY DIFFRACTIONr_mcbond_it2.881.5214
X-RAY DIFFRACTIONr_mcangle_it4.9642341
X-RAY DIFFRACTIONr_scbond_it5.4523175
X-RAY DIFFRACTIONr_scangle_it8.5144.5182
X-RAY DIFFRACTIONr_rigid_bond_restr2.9263389
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 46 -
Rwork0.29 416 -
all-462 -
obs--100 %

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