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- PDB-2nlb: Human beta-defensin-1 (Mutant Asn4Ala) -

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Basic information

Entry
Database: PDB / ID: 2nlb
TitleHuman beta-defensin-1 (Mutant Asn4Ala)
ComponentsBeta-defensin 1
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / chemotactic / defensin
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: 1.85 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 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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 1.6Nov 6, 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
C: Beta-defensin 1
D: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0719
Polymers15,5904
Non-polymers4805
Water3,891216
1
A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1864
Polymers3,8981
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)3,8981
Polymers3,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)3,8981
Polymers3,8981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-defensin 1
hetero molecules


  • defined by author
  • 4.09 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)4,0903
Polymers3,8981
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Beta-defensin 1
hetero molecules

C: Beta-defensin 1

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


Theoretical massNumber of molelcules
Total (without water)16,0719
Polymers15,5904
Non-polymers4805
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
crystal symmetry operation2_546-x,y-1/2,-z+11
Buried area3660 Å2
ΔGint-101 kcal/mol
Surface area8370 Å2
MethodPISA
6
A: Beta-defensin 1
hetero molecules

C: Beta-defensin 1


Theoretical massNumber of molelcules
Total (without water)8,0835
Polymers7,7952
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
Buried area1330 Å2
ΔGint-51 kcal/mol
Surface area4790 Å2
MethodPISA
7
B: Beta-defensin 1
D: Beta-defensin 1
hetero molecules


  • defined by software
  • 7.99 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)7,9874
Polymers7,7952
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-38 kcal/mol
Surface area4820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.520, 26.400, 57.530
Angle α, β, γ (deg.)90.00, 100.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer

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Components

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


Mass: 3897.573 Da / Num. of mol.: 4 / Fragment: human beta-defensin 1, residues 33-68 / Mutation: N4A
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.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: PEG 8000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.5, 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: Aug 14, 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: 12053 / Num. obs: 12053 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.08 / Χ2: 0.968 / Net I/σ(I): 17.1
Reflection shellResolution: 1.85→1.92 Å / Redundancy: 5 % / Rmerge(I) obs: 0.255 / Mean I/σ(I) obs: 6 / Num. unique all: 1178 / Χ2: 0.951 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.401data extraction
HKL-2000data 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: 0.952 / Cor.coef. Fo:Fc free: 0.912 / SU B: 5.432 / SU ML: 0.098 / SU R Cruickshank DPI: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.153 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 577 4.8 %RANDOM
Rwork0.179 ---
all0.182 12045 --
obs0.182 12045 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.632 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.84 Å2
2---0.21 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1072 0 25 216 1313
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01611360.022
X-RAY DIFFRACTIONr_angle_refined_deg1.52315301.98
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5061405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.7443622.222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61219615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.592415
X-RAY DIFFRACTIONr_chiral_restr0.0941560.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0078080.02
X-RAY DIFFRACTIONr_nbd_refined0.2294910.2
X-RAY DIFFRACTIONr_nbtor_refined0.3027840.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1841730.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1741070.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.236450.2
X-RAY DIFFRACTIONr_mcbond_it1.0137361.5
X-RAY DIFFRACTIONr_mcangle_it1.48311332
X-RAY DIFFRACTIONr_scbond_it2.234703
X-RAY DIFFRACTIONr_scangle_it3.1693974.5
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 42 -
Rwork0.231 800 -
obs-842 97.12 %
Refinement TLS params.Origin x: 9.0413 Å / Origin y: 12.1258 Å / Origin z: 19.7823 Å
111213212223313233
T-0.0719 Å20.0258 Å2-0.0035 Å2--0.0688 Å20.005 Å2---0.0258 Å2
L0.4372 °20.3007 °20.194 °2-0.2068 °20.1334 °2--0.086 °2
S-0.0364 Å °0.0691 Å °-0.0109 Å °-0.0889 Å °0.0186 Å °-0.0123 Å °-0.0146 Å °0.0193 Å °0.0178 Å °
Refinement TLS groupSelection: ALL

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