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- PDB-2nlc: Human beta-defensin-1 (mutant Ser8Ala) -

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Basic information

Entry
Database: PDB / ID: 2nlc
TitleHuman beta-defensin-1 (mutant Ser8Ala)
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 / cAMP-mediated signaling / : / sperm midpiece / 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 / cAMP-mediated signaling / : / sperm midpiece / 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
ACETATE ION / Beta-defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 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

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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)16,33411
Polymers15,6984
Non-polymers6357
Water3,855214
1
A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0212
Polymers3,9251
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,1173
Polymers3,9251
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,0803
Polymers3,9251
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Beta-defensin 1
hetero molecules


  • defined by author&software
  • 4.12 kDa, 1 polymers
Theoretical massNumber of molelcules
Total (without water)4,1173
Polymers3,9251
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Beta-defensin 1
hetero molecules

A: Beta-defensin 1
hetero molecules

B: Beta-defensin 1
hetero molecules

C: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,33411
Polymers15,6984
Non-polymers6357
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_566x,y+1,z+11
crystal symmetry operation1_556x,y,z+11
crystal symmetry operation1_456x-1,y,z+11
Buried area3520 Å2
ΔGint-119 kcal/mol
Surface area8980 Å2
MethodPISA
6
C: Beta-defensin 1
hetero molecules

A: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1005
Polymers7,8492
Non-polymers2513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area1430 Å2
ΔGint-50 kcal/mol
Surface area4910 Å2
MethodPISA
7
B: Beta-defensin 1
hetero molecules

D: Beta-defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2336
Polymers7,8492
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area1280 Å2
ΔGint-49 kcal/mol
Surface area4880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)25.740, 33.190, 41.850
Angle α, β, γ (deg.)73.90, 85.50, 86.20
Int Tables number1
Space group name H-MP1
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: 3924.598 Da / Num. of mol.: 4 / Fragment: HUMAN BETA-DEFENSIN 1, residues 33-68 / Mutation: S8A
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: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7
Details: PEG 8000, LITHIUM SULFATE, pH 7.0, 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 10, 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: 1.65→30 Å / Num. all: 14783 / Num. obs: 14783 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.051 / Χ2: 0.958 / Net I/σ(I): 29
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 5 % / Rmerge(I) obs: 0.207 / Mean I/σ(I) obs: 6.4 / Num. unique all: 1367 / Χ2: 1.046 / % possible all: 85.8

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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: 1.65→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.086 / SU ML: 0.068 / SU R Cruickshank DPI: 0.113 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.204 732 5 %RANDOM
Rwork0.166 ---
all0.168 14783 --
obs0.168 14783 92.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.276 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.03 Å2-0.67 Å2
2--0.79 Å2-0.3 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 34 214 1340
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.01911510.022
X-RAY DIFFRACTIONr_angle_refined_deg1.66615511.98
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8451405
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.184023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.36519615
X-RAY DIFFRACTIONr_dihedral_angle_4_deg28.311415
X-RAY DIFFRACTIONr_chiral_restr0.1191560.2
X-RAY DIFFRACTIONr_gen_planes_refined0.0088280.02
X-RAY DIFFRACTIONr_nbd_refined0.234960.2
X-RAY DIFFRACTIONr_nbtor_refined0.3077820.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1421600.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.271070.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.201380.2
X-RAY DIFFRACTIONr_mcbond_it1.357361.5
X-RAY DIFFRACTIONr_mcangle_it1.92611332
X-RAY DIFFRACTIONr_scbond_it2.9994833
X-RAY DIFFRACTIONr_scangle_it3.9294184.5
X-RAY DIFFRACTIONRIGID-BOND RESTRAINTS (A**2)2.02123
X-RAY DIFFRACTIONSPHERICITY; BONDED ATOMS (A**2)305.702
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 52 -
Rwork0.278 942 -
obs-994 83.67 %

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