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- PDB-3hjd: X-ray structure of monomeric variant of HNP1 -

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Basic information

Entry
Database: PDB / ID: 3hjd
TitleX-ray structure of monomeric variant of HNP1
ComponentsHuman neutrophil peptide 1
KeywordsANTIMICROBIAL PROTEIN / HNP1 / monomeric defensin / antimicrobial / chemotactic / Antibiotic / Antiviral defense / Fungicide
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 / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / defense response to virus / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / 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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLubkowski, J. / Pazgier, M. / Lu, W.
CitationJournal: To be Published
Title: What Dictates the Multifaced Functions of the Human alpha-Defensin HNP?
Authors: Wei, G. / de Leeuw, E. / Pazgier, M. / Rajabi, M. / Li, J. / Zou, G. / Ericksen, B. / Wu, Z. / Yuan, W. / Szmacinski, H. / Lu, W.-Y. / Lubkowski, J. / Lehrer, R.L. / Lu, W.
History
DepositionMay 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Advisory
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 6, 2024Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Human neutrophil peptide 1
B: Human neutrophil peptide 1


Theoretical massNumber of molelcules
Total (without water)6,9322
Polymers6,9322
Non-polymers00
Water1,31573
1
A: Human neutrophil peptide 1


Theoretical massNumber of molelcules
Total (without water)3,4661
Polymers3,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Human neutrophil peptide 1


Theoretical massNumber of molelcules
Total (without water)3,4661
Polymers3,4661
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.85, 69.85, 46.33
Angle α, β, γ (deg.)90, 90, 120
Int Tables number177
Space group name H-MP622
Components on special symmetry positions
IDModelComponents
11A-231-

HOH

DetailsEach of two monomers present in the asymmetric unit represents half of the biological assembly. Biologically-relevant dimers are not present in crystals of this derivative

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Components

#1: Protein/peptide Human neutrophil peptide 1 / Neutrophil defensin 1 / HNP-1 / HP-1 / HP1 / Defensin / alpha 1 / HP 1-56 / Neutrophil defensin 2 / ...Neutrophil defensin 1 / HNP-1 / HP-1 / HP1 / Defensin / alpha 1 / HP 1-56 / Neutrophil defensin 2 / HNP-2 / HP-2 / HP2


Mass: 3466.137 Da / Num. of mol.: 2 / Fragment: Residues 65-94 / Mutation: ILE84IML / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES-Na (pH 7.5), 0.2 M sodium citrate, 30% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 10, 2007
Details: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si 220. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→27.89 Å / Num. all: 8402 / Num. obs: 8402 / % possible obs: 99.4 % / Observed criterion σ(F): -1.74 / Observed criterion σ(I): -3 / Redundancy: 13 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 16.4
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 11 % / Rmerge(I) obs: 0.476 / Mean I/σ(I) obs: 4.2 / Num. unique all: 831 / Rsym value: 0.476 / % possible all: 99.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.4.0057refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFN

1dfn


Resolution: 1.65→15 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.276 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20313 391 4.7 %RANDOM
Rwork0.1741 ---
all0.17544 8003 --
obs0.17544 8003 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.718 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.62 Å20 Å2
2--1.23 Å20 Å2
3----1.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.297 Å / Luzzati d res low obs: 15 Å
Refinement stepCycle: LAST / Resolution: 1.65→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms476 0 0 73 549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022496
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0111.964666
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.705554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.21618.18222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7721570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.651158
X-RAY DIFFRACTIONr_chiral_restr0.1630.266
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021370
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.381.5295
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.2782460
X-RAY DIFFRACTIONr_scbond_it3.0393201
X-RAY DIFFRACTIONr_scangle_it4.7394.5206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 25 -
Rwork0.198 554 -
obs-579 97.31 %
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)
16.2849-0.209-0.8311.1021-0.12383.1478-0.0534-0.07570.11240.07110.04390.0293-0.01140.13640.0096-0.01520.0003-0.0162-0.0625-0.0086-0.007323.058940.259831.7062
21.5674-0.56520.96170.5533-0.94722.8464-0.0194-0.0419-0.0382-0.02060.0366-0.02340.00450.0521-0.01730.0079-0.0054-0.014-0.0263-0.0042-0.03017.758847.136334.3924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 31
2X-RAY DIFFRACTION2B2 - 31

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