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- PDB-1zmi: Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA... -

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Basic information

Entry
Database: PDB / ID: 1zmi
TitleCrystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 space group )
ComponentsNeutrophil defensin 2
KeywordsANTIMICROBIAL PROTEIN / ALPHA-DEFENSIN / ANTIMICROBIAL / D-AMINO ACID SUBSTITUTION
Function / homology
Function and homology information


Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / 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 / azurophil granule lumen ...Defensins / disruption of plasma membrane integrity in another organism / Alpha-defensins / 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 / 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 / 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
Neutrophil defensin 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 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: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 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 1.5Aug 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)14,23711
Polymers13,5804
Non-polymers6577
Water2,198122
1
A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4479
Polymers6,7902
Non-polymers6577
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-24 kcal/mol
Surface area4010 Å2
MethodPISA
2
C: Neutrophil defensin 2
D: Neutrophil defensin 2


Theoretical massNumber of molelcules
Total (without water)6,7902
Polymers6,7902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1050 Å2
ΔGint-24 kcal/mol
Surface area4280 Å2
MethodPISA
3
A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules

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

C: Neutrophil defensin 2
D: Neutrophil defensin 2

C: Neutrophil defensin 2
D: Neutrophil defensin 2


Theoretical massNumber of molelcules
Total (without water)28,47422
Polymers27,1608
Non-polymers1,31314
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
crystal symmetry operation2_554-y,x-y,z-1/31
crystal symmetry operation4_556y,x,-z+11
Buried area10020 Å2
ΔGint-135 kcal/mol
Surface area12270 Å2
MethodPISA
4
A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules

C: Neutrophil defensin 2
D: Neutrophil defensin 2


Theoretical massNumber of molelcules
Total (without water)14,23711
Polymers13,5804
Non-polymers6577
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area3780 Å2
ΔGint-62 kcal/mol
Surface area7370 Å2
MethodPISA
5
A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules

C: Neutrophil defensin 2
D: Neutrophil defensin 2


Theoretical massNumber of molelcules
Total (without water)14,23711
Polymers13,5804
Non-polymers6577
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_566x-y,-y+1,-z+4/31
Buried area3610 Å2
ΔGint-57 kcal/mol
Surface area7540 Å2
MethodPISA
6
A: Neutrophil defensin 2
B: Neutrophil defensin 2
hetero molecules

C: Neutrophil defensin 2
D: Neutrophil defensin 2


Theoretical massNumber of molelcules
Total (without water)14,23711
Polymers13,5804
Non-polymers6577
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-y,x-y,z-1/31
Buried area3570 Å2
ΔGint-52 kcal/mol
Surface area7570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.685, 71.685, 54.882
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein/peptide
Neutrophil defensin 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 3 Å3/Da / Density % sol: 58.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: lithium sulfate, PEG8000, VAPOR DIFFUSION, 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: 1.15→30 Å / Num. all: 57187 / Num. obs: 57187 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rsym value: 0.09 / Net I/σ(I): 17
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.513 / % possible all: 90.4

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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 code 1DFN)

1dfn


Resolution: 1.15→12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.774 / SU ML: 0.017 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.031 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18202 2891 5.1 %RANDOM
Rwork0.16807 ---
obs0.16876 54227 98.53 %-
all-54227 --
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: 14.858 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.15→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms936 0 39 122 1097
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221006
X-RAY DIFFRACTIONr_bond_other_d0.0020.02891
X-RAY DIFFRACTIONr_angle_refined_deg1.891.9641361
X-RAY DIFFRACTIONr_angle_other_deg1.8432032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0255112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.98718.18244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.24115145
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6481516
X-RAY DIFFRACTIONr_chiral_restr0.4130.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021080
X-RAY DIFFRACTIONr_gen_planes_other00.02260
X-RAY DIFFRACTIONr_nbd_refined0.1970.3137
X-RAY DIFFRACTIONr_nbd_other0.2390.3813
X-RAY DIFFRACTIONr_nbtor_refined0.2010.5424
X-RAY DIFFRACTIONr_nbtor_other0.0890.5637
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2230.5158
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.060.51
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.30.39
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.3105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.531
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1982594
X-RAY DIFFRACTIONr_mcbond_other1.1162244
X-RAY DIFFRACTIONr_mcangle_it2.8873914
X-RAY DIFFRACTIONr_scbond_it3.022498
X-RAY DIFFRACTIONr_scangle_it3.7853447
X-RAY DIFFRACTIONr_rigid_bond_restr1.65932243
X-RAY DIFFRACTIONr_sphericity_free9.573122
X-RAY DIFFRACTIONr_sphericity_bonded3.72131865
LS refinement shellResolution: 1.15→1.212 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.207 411 -
Rwork0.184 7245 -
obs--92.23 %
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)
11.76460.27690.78323.1093-1.31673.03840.0765-0.0672-0.0720.0438-0.03740.09250.1025-0.0869-0.0391-0.0284-0.01440.006-0.02720.0028-0.0179-12.749529.850926.3762
23.6585-1.5905-1.04172.72750.82893.5518-0.10070.2469-0.3560.0385-0.17010.28620.2184-0.30210.2708-0.036-0.01450.0308-0.0036-0.04220.009319.912110.00141.8245
31.0248-0.716-1.06761.66871.42112.9649-0.008-0.04650.05560.04940.0507-0.10380.04660.1501-0.0427-0.0216-0.0055-0.0049-0.0151-0.0002-0.0128-0.824535.552925.7336
43.6638-1.75-0.77036.0841-1.75084.1569-0.19860.0437-0.05530.21570.09950.2664-0.0622-0.11820.0991-0.04220.02460.0364-0.0291-0.0038-0.022915.865815.973751.1493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 291 - 29
2X-RAY DIFFRACTION2CC1 - 291 - 29
3X-RAY DIFFRACTION3BB1 - 291 - 29
4X-RAY DIFFRACTION4DD19 - 2919 - 29

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