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- PDB-2pm5: Human alpha-defensin 1 derivative (HNP1) -

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Basic information

Entry
Database: PDB / ID: 2pm5
TitleHuman alpha-defensin 1 derivative (HNP1)
ComponentsNeutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)
KeywordsANTIMICROBIAL PROTEIN / defensin / antimicrobial / derivative
Function / homology
Function and homology information


pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / estrogen receptor signaling pathway / defense response to fungus / extracellular matrix ...pore-forming activity / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / estrogen receptor signaling pathway / defense response to fungus / extracellular matrix / innate immune response in mucosa / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / chemotaxis / azurophil granule lumen / antibacterial humoral response / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / 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 / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
PHOSPHATE ION / Neutrophil defensin 1 / Neutrophil defensin 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLubkowski, J. / Pazgier, M. / Lu, W.
CitationJournal: To be Published
Title: Human alpha-defensin 1 derivative (HNP1)
Authors: Lubkowski, J. / Lu, W. / Zou, G. / de Leeuw, E. / Li, C. / Pazgier, M. / Zeng, P. / Lu, W.Y.
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 / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 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

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8293
Polymers6,7342
Non-polymers951
Water1,04558
1
A: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,4622
Polymers3,3671
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)


Theoretical massNumber of molelcules
Total (without water)3,3671
Polymers3,3671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)

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

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)13,4684
Polymers13,4684
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_765-x+2,-y+1,z1
crystal symmetry operation5_756-x+2,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
Buried area2110 Å2
ΔGint-25 kcal/mol
Surface area7760 Å2
MethodPISA
4
A: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)
hetero molecules

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

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

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


Theoretical massNumber of molelcules
Total (without water)13,8488
Polymers13,4684
Non-polymers3804
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z+1/21
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area3220 Å2
ΔGint-52 kcal/mol
Surface area7230 Å2
MethodPISA
5
A: Neutrophil defensin 1 (HNP-1) (HP-1) (HP1) (Defensin, alpha 1)
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)6,9244
Polymers6,7342
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area1200 Å2
ΔGint-21 kcal/mol
Surface area4030 Å2
MethodPISA
6
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)6,7342
Polymers6,7342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,-y+1,-z+11
Buried area690 Å2
ΔGint-7 kcal/mol
Surface area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.409, 57.409, 96.967
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number93
Space group name H-MP4222

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Components

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


Mass: 3366.977 Da / Num. of mol.: 2 / Mutation: Arg14->Orn, Arg15->Orn, Arg24->Orn
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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M sodium citrate tribasic dihydrate, pH 5.6, 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 4, 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: 2.4→30 Å / Num. all: 6220 / Num. obs: 6220 / % possible obs: 91.1 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 31.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.518 / Mean I/σ(I) obs: 2.1 / Num. unique all: 351 / Rsym value: 0.518 / % possible all: 53.8

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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: 2.4→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.967 / SU B: 11.767 / SU ML: 0.138 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.189 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21789 284 4.6 %RANDOM
Rwork0.20024 ---
all0.20106 5868 --
obs0.20106 5868 90.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.758 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å20 Å20 Å2
2--3.25 Å20 Å2
3----6.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms464 0 5 58 527
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022486
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.741.951660
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.228558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.43822.22218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2341574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.618152
X-RAY DIFFRACTIONr_chiral_restr0.1380.264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02364
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.2178
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.2314
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2120.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7271.5305
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.3542468
X-RAY DIFFRACTIONr_scbond_it1.5493224
X-RAY DIFFRACTIONr_scangle_it2.2144.5192
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.402→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 15 -
Rwork0.364 233 -
obs--52.21 %
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)
111.1002-2.05094.02176.6469-2.520414.5568-0.2758-0.0818-0.0328-0.31110.3444-0.135-0.01930.6653-0.0686-0.228-0.09430.05410.0539-0.0373-0.213235.089229.262934.5853
29.29383.9229-3.53296.4871-2.280815.0828-0.7025-0.3266-0.571-0.14850.3482-0.52040.73141.99040.3543-0.16910.25390.0240.70670.0228-0.006747.052524.046453.2319
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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