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- PDB-2nlf: Human beta-defensin-1 (Mutant Leu13Glu) -

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Basic information

Entry
Database: PDB / ID: 2nlf
TitleHuman beta-defensin-1 (Mutant Leu13Glu)
ComponentsBeta-defensin 1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / chemotactic / defensin / mutant
Function / homology
Function and homology information


positive regulation of flagellated sperm motility involved in capacitation / CCR6 chemokine receptor binding / microvesicle / 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 / CCR6 chemokine receptor binding / microvesicle / 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 / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1, 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
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)8,2976
Polymers7,9132
Non-polymers3844
Water4,125229
1
A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1493
Polymers3,9571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1493
Polymers3,9571
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Beta-defensin 1
hetero molecules

A: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,59512
Polymers15,8264
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
crystal symmetry operation3_544x+1/2,y-1/2,z-11
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area3210 Å2
ΔGint-139 kcal/mol
Surface area9720 Å2
MethodPISA
4
A: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2976
Polymers7,9132
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
Buried area1230 Å2
ΔGint-47 kcal/mol
Surface area5050 Å2
MethodPISA
5
A: Beta-defensin 1
hetero molecules

A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2976
Polymers7,9132
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area780 Å2
ΔGint-51 kcal/mol
Surface area5720 Å2
MethodPISA
6
B: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2976
Polymers7,9132
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area1060 Å2
ΔGint-54 kcal/mol
Surface area5370 Å2
MethodPISA
7
B: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2976
Polymers7,9132
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_557-x,y,-z+21
Buried area1100 Å2
ΔGint-75 kcal/mol
Surface area5710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.010, 46.790, 28.560
Angle α, β, γ (deg.)90.00, 97.30, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-400-

HOH

21B-400-

HOH

DetailsBiological assembly is a monomer

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Components

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


Mass: 3956.554 Da / Num. of mol.: 2 / Fragment: Human beta-defensin 1, residues 33-68 / Mutation: L13E
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


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.: 229 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.6
Details: PEG 4000, AMMONIUM SULFATE, SODIUM ACETATE, pH 4.6, 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 10, 2004 / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. all: 13851 / Num. obs: 13851 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.07 / Χ2: 0.977 / Net I/σ(I): 18
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 5.8 / Num. unique all: 1365 / Χ2: 0.956 / % possible all: 97.2

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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: 1.45→30 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.051 / SU ML: 0.037 / SU R Cruickshank DPI: 0.081 / Cross valid method: THROUGHOUT / ESU R Free: 0.07 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.184 988 7.1 %RANDOM
Rwork0.14 ---
all0.143 13844 --
obs0.143 13844 98.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.457 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.01 Å2
2---0.11 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms574 0 20 230 824
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.0186100.022
X-RAY DIFFRACTIONr_angle_refined_deg1.6728301.984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25705
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.7432223.636
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.30710615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg32.131215
X-RAY DIFFRACTIONr_chiral_restr0.113860.2
X-RAY DIFFRACTIONr_gen_planes_refined0.014360.02
X-RAY DIFFRACTIONr_nbd_refined0.253320.2
X-RAY DIFFRACTIONr_nbtor_refined0.3024280.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1631960.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.203480.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.155460.2
X-RAY DIFFRACTIONr_mcbond_it1.8713811.5
X-RAY DIFFRACTIONr_mcangle_it2.5126082
X-RAY DIFFRACTIONr_scbond_it3.4272673
X-RAY DIFFRACTIONr_scangle_it4.4242224.5
X-RAY DIFFRACTIONRIGID-BOND RESTRAINTS (A**2)1.9876483
X-RAY DIFFRACTIONSPHERICITY; FREE ATOMS (A**2)2307.425
X-RAY DIFFRACTIONSPHERICITY; BONDED ATOMS (A**2)5944.462
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 68 -
Rwork0.186 924 -
obs-992 97.06 %

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