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- PDB-2pm4: Human alpha-defensin 1 (multiple Arg->Lys mutant) -

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Basic information

Entry
Database: PDB / ID: 2pm4
TitleHuman alpha-defensin 1 (multiple Arg->Lys mutant)
ComponentsNeutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)
KeywordsANTIMICROBIAL PROTEIN / antimicrobial / defensin / mutant
Function / homology
Function and homology information


pore-forming activity / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa ...pore-forming activity / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa / Golgi lumen / chemotaxis / antimicrobial humoral immune response mediated by antimicrobial peptide / azurophil granule lumen / antibacterial humoral response / : / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / defense response to virus / killing of cells of another organism / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Mammalian defensins signature. / Alpha-defensin, C-terminal / Mammalian defensin / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
Neutrophil defensin 1 / Neutrophil defensin 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 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: Advisory / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 6, 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: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)
B: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)


Theoretical massNumber of molelcules
Total (without water)6,8242
Polymers6,8242
Non-polymers00
Water1,62190
1
A: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)

A: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)


Theoretical massNumber of molelcules
Total (without water)6,8242
Polymers6,8242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
2
B: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)

B: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)


Theoretical massNumber of molelcules
Total (without water)6,8242
Polymers6,8242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Unit cell
Length a, b, c (Å)41.383, 41.383, 97.165
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222
Components on special symmetry positions
IDModelComponents
11B-45-

HOH

Detailsbiological dimer is formed by chain B and its symmetry related by operator -x,-y,z

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Components

#1: Protein/peptide Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)


Mass: 3412.079 Da / Num. of mol.: 2 / Mutation: Arg14->Lys, Arg15->Lys, Arg24->Lys
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFA1, DEF1, DEFA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P59665, UniProt: P59666*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / 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: 3.05 Å3/Da / Density % sol: 59.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.4 M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 2, 2007 / Details: mirrors
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→30 Å / Num. all: 6505 / Num. obs: 6505 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 21
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 3.1 / Num. unique all: 610 / Rsym value: 0.412 / % possible all: 95.5

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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: 1DFN

1dfn


Resolution: 1.95→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 6.802 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.145 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 306 4.7 %RANDOM
Rwork0.19222 ---
all0.19479 6190 --
obs0.19479 6190 97.36 %-
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: 49.312 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.3333 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms470 0 0 90 560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022488
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.957660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.148558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.68922.22218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.9871580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.618152
X-RAY DIFFRACTIONr_chiral_restr0.1580.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02364
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.2170
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2323
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2470.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0941.5304
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6442468
X-RAY DIFFRACTIONr_scbond_it2.6793228
X-RAY DIFFRACTIONr_scangle_it3.3814.5192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.949→1.999 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 18 -
Rwork0.245 432 -
obs--96.15 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.49774.8531-1.299811.72061.18964.5792-0.1420.0878-0.3918-0.5252-0.009-0.1991-0.03940.04660.1511-0.18870.02390.037-0.24250.0422-0.1808-16.319710.356219.3084
25.4343-5.043-4.702917.157510.335311.07250.0315-0.1843-0.13160.29770.38490.22380.05370.0402-0.4165-0.19550.04010.0514-0.11990.0534-0.2485-4.89024.19310.5004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 301 - 30
2X-RAY DIFFRACTION2BB1 - 301 - 30

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