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- PDB-1zmh: Crystal structure of human neutrophil peptide 2, HNP-2 (variant G... -

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Basic information

Entry
Database: PDB / ID: 1zmh
TitleCrystal structure of human neutrophil peptide 2, HNP-2 (variant Gly16-> D-Ala)
ComponentsNeutrophil defensin 2
KeywordsANTIMICROBIAL PROTEIN / alpha-defensin / D-amino acid substitution
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / Defensins / Alpha-defensins / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa / Golgi lumen / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response ...disruption of plasma membrane integrity in another organism / Defensins / Alpha-defensins / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa / Golgi lumen / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to virus / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / 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 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLubkowski, J. / Prahl, A. / Lu, W.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Reconstruction of the conserved beta-bulge in mammalian defensins using D-amino acids.
Authors: Xie, C. / Prahl, A. / Ericksen, B. / Wu, Z. / Zeng, P. / Li, X. / Lu, W.Y. / Lubkowski, J. / Lu, W.
History
DepositionMay 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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 1.5Aug 23, 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 2
B: Neutrophil defensin 2
C: Neutrophil defensin 2
D: Neutrophil defensin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,33510
Polymers13,5804
Non-polymers7556
Water1,964109
1
A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2615
Polymers6,7902
Non-polymers4703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neutrophil defensin 2
D: Neutrophil defensin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0745
Polymers6,7902
Non-polymers2843
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-27 kcal/mol
Surface area4160 Å2
MethodPISA
3
A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules

A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,52110
Polymers13,5804
Non-polymers9416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4470 Å2
ΔGint-42 kcal/mol
Surface area7440 Å2
MethodPISA
4
C: Neutrophil defensin 2
D: Neutrophil defensin 2
hetero molecules

C: Neutrophil defensin 2
D: Neutrophil defensin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,14910
Polymers13,5804
Non-polymers5686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area3380 Å2
ΔGint-65 kcal/mol
Surface area7500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.038, 26.051, 61.587
Angle α, β, γ (deg.)90.00, 105.79, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-39-

HOH

21C-435-

HOH

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Components

#1: Protein/peptide
Neutrophil defensin 2 / HNP-2


Mass: 3395.059 Da / Num. of mol.: 4 / Mutation: G16(DAL)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEFA3, DEF3 / Production host: Escherichia coli (E. coli) / References: UniProt: P59666
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: lithium sulfate, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 10, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. all: 20719 / Num. obs: 20719 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.038
Reflection shellResolution: 1.48→1.55 Å / % possible all: 65.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BASED ON MONOMER OF HNP-3 (PDB ENTRY 1DEF)

1def


Resolution: 1.5→19 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.676 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21252 1022 5.1 %RANDOM
Rwork0.17734 ---
all0.179 19047 --
obs0.17921 19047 95.6 %-
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: 26.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.03 Å2
2--0.06 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 46 109 1091
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221008
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9711360
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5165112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.47417.90743
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.78315142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1721516
X-RAY DIFFRACTIONr_chiral_restr0.1410.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02752
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.3425
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3310.5685
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.369
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3510.564
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9452587
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.9763911
X-RAY DIFFRACTIONr_scbond_it3.2762500
X-RAY DIFFRACTIONr_scangle_it4.2673449
X-RAY DIFFRACTIONr_rigid_bond_restr2.46731087
X-RAY DIFFRACTIONr_sphericity_free9.973111
X-RAY DIFFRACTIONr_sphericity_bonded5.6733978
LS refinement shellResolution: 1.5→1.581 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.224 122 -
Rwork0.141 2226 -
obs--77.9 %
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)
13.55970.14611.43780.8835-0.44261.93810.0354-0.0064-0.2264-0.026-0.086-0.05210.11690.01820.0505-0.0120.03370.01650.01120.0253-0.026810.3019-5.5531-0.1274
22.4086-0.702-1.66311.13120.43214.45760.16150.04710.21240.0204-0.0629-0.0519-0.09480.0734-0.0986-0.01830.00310.0134-0.00580.0342-0.027513.67864.57198.2339
30.493-0.0558-0.83681.03410.46561.88380.0432-0.00180.0609-0.0091-0.01190.0177-0.0331-0.0219-0.03140.01820.00170.0114-0.02140.0041-0.013525.749330.18436.9474
43.64630.27911.00350.7361-0.53351.94610.02430.0936-0.0382-0.01280.06540.0253-0.0017-0.0952-0.08970.00580.00890.0001-0.02280.0035-0.02222.321819.727529.6211
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 291 - 29
2X-RAY DIFFRACTION2BB1 - 291 - 29
3X-RAY DIFFRACTION3CC1 - 291 - 29
4X-RAY DIFFRACTION4DD1 - 291 - 29

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