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- PDB-2nlp: Human beta-defensin-1 (Mutant Gln24Glu) -

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Basic information

Entry
Database: PDB / ID: 2nlp
TitleHuman beta-defensin-1 (Mutant Gln24Glu)
ComponentsBeta-defensin 1Beta defensin
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / chemotactic / defensin / mutant
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 / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium ...positive regulation of flagellated sperm motility involved in capacitation / microvesicle / CCR6 chemokine receptor binding / Beta defensins / Defensins / : / sperm midpiece / cAMP-mediated signaling / innate immune response in mucosa / response to bacterium / 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 / membrane / identical protein binding
Similarity search - Function
Beta defensin type / Beta defensin
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLubkowski, J. / Pazgier, M.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Studies of the Biological Properties of Human beta-Defensin 1.
Authors: Pazgier, M. / Prahl, A. / Hoover, D.M. / Lubkowski, J.
History
DepositionOct 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 5, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)16,34310
Polymers15,7664
Non-polymers5766
Water4,954275
1
A: Beta-defensin 1
hetero molecules


  • defined by author&software
  • 4.33 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)4,3265
Polymers3,9421
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0382
Polymers3,9421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)3,9421
Polymers3,9421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0382
Polymers3,9421
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
A: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules

C: Beta-defensin 1
D: Beta-defensin 1
hetero molecules


  • defined by software
  • 16.3 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)16,34310
Polymers15,7664
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area3420 Å2
ΔGint-110 kcal/mol
Surface area8850 Å2
MethodPISA
6
A: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules


  • defined by software
  • 8.36 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)8,3637
Polymers7,8832
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
Buried area1490 Å2
ΔGint-62 kcal/mol
Surface area4840 Å2
MethodPISA
7
C: Beta-defensin 1
D: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9793
Polymers7,8832
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-37 kcal/mol
Surface area4790 Å2
MethodPISA
8
B: Beta-defensin 1
hetero molecules

C: Beta-defensin 1
D: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0175
Polymers11,8253
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2280 Å2
ΔGint-73 kcal/mol
Surface area6860 Å2
MethodPISA
9
A: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules

C: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)12,3058
Polymers11,8253
Non-polymers4805
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445x-1/2,y-1/2,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area2270 Å2
ΔGint-86 kcal/mol
Surface area7010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.680, 27.680, 58.230
Angle α, β, γ (deg.)90.00, 113.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-313-

HOH

DetailsBiological assembly is a monomer

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Components

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


Mass: 3941.583 Da / Num. of mol.: 4 / Fragment: human beta-defensin 1, residues 33-68 / Mutation: Q24E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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 / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.29 Å3/Da / Density % sol: 46.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: LITHIUM SULFATE, HEPES, pH 7.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2005 / Details: Osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 12081 / Num. obs: 12081 / % possible obs: 96.4 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Rmerge(I) obs: 0.058 / Χ2: 1.009 / Net I/σ(I): 27
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 6.1 / Num. unique all: 1143 / Χ2: 1.057 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
MAR345345DTBdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IJV

1ijv


Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.266 / SU ML: 0.102 / SU R Cruickshank DPI: 0.162 / Cross valid method: THROUGHOUT / ESU R Free: 0.157 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 582 4.8 %RANDOM
Rwork0.176 ---
all0.179 12078 --
obs0.179 12078 96.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.923 Å2
Baniso -1Baniso -2Baniso -3
1--1.49 Å20 Å2-1.07 Å2
2--1.19 Å20 Å2
3----0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 30 278 1392
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01811400.022
X-RAY DIFFRACTIONr_angle_refined_deg1.69815361.986
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2371405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.6034023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.86119215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.071415
X-RAY DIFFRACTIONr_chiral_restr0.1081520.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0078240.02
X-RAY DIFFRACTIONr_nbd_refined0.2474850.2
X-RAY DIFFRACTIONr_nbtor_refined0.3067620.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.211670.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2181170.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.199790.2
X-RAY DIFFRACTIONr_mcbond_it1.127271.5
X-RAY DIFFRACTIONr_mcangle_it1.78111242
X-RAY DIFFRACTIONr_scbond_it2.8374773
X-RAY DIFFRACTIONr_scangle_it4.0594124.5
LS refinement shellResolution: 1.848→1.896 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 30 -
Rwork0.235 814 -
obs-844 92.65 %

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