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- PDB-2plz: Arg-modified human beta-defensin 1 (HBD1) -

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Basic information

Entry
Database: PDB / ID: 2plz
TitleArg-modified human beta-defensin 1 (HBD1)
ComponentsBeta-defensin 1
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL / CHEMOTACTIC / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsLubkowski, J. / Pazgier, M. / Lu, W.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Toward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs.
Authors: Zou, G. / de Leeuw, E. / Li, C. / Pazgier, M. / Li, C. / Zeng, P. / Lu, W.Y. / Lubkowski, J. / Lu, W.
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,4375
Polymers4,0531
Non-polymers3844
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)20.366, 27.408, 55.079
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 / BD-1 / Defensin / beta 1 / hBD-1


Mass: 4052.654 Da / Num. of mol.: 1 / Mutation: Lys22Arg, Lys31Arg, Lys33Arg, Lys36Arg
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Strain: DEFB1, BD1, HBD1 / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 35.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.0 M Lithium sulfate, 2% (w/v) PEG8000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.96 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2007 / Details: mirrors
RadiationMonochromator: SI crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.36→30 Å / Num. all: 7002 / Num. obs: 7002 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Rmerge(I) obs: 0.087 / Rsym value: 0.087 / Net I/σ(I): 17
Reflection shellResolution: 1.36→1.41 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 4.2 / Num. unique all: 657 / Rsym value: 0.341 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2IJV

2ijv


Resolution: 1.36→20 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.271 / SU ML: 0.024 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.05 / ESU R Free: 0.052 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15797 332 4.8 %RANDOM
Rwork0.10528 ---
all0.10776 7002 --
obs0.10776 6636 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--0.66 Å20 Å2
3---0.01 Å2
Refine analyzeLuzzati coordinate error obs: 0.1154 Å
Refinement stepCycle: LAST / Resolution: 1.36→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms279 0 20 81 380
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021303
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.996411
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.639535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.89619.28614
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.4971544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.509155
X-RAY DIFFRACTIONr_chiral_restr0.1130.238
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.02226
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2109
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2203
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1920.224
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2140.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4021.5182
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0762281
X-RAY DIFFRACTIONr_scbond_it4.2533136
X-RAY DIFFRACTIONr_scangle_it5.9114.5130
X-RAY DIFFRACTIONr_rigid_bond_restr2.3593318
X-RAY DIFFRACTIONr_sphericity_free9.528381
X-RAY DIFFRACTIONr_sphericity_bonded5.3243299
LS refinement shellResolution: 1.363→1.398 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 27 -
Rwork0.131 440 -
obs--98.32 %

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