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- PDB-6dmm: Crystal structure of the G23A mutant of human alpha defensin HNP4. -

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Basic information

Entry
Database: PDB / ID: 6dmm
TitleCrystal structure of the G23A mutant of human alpha defensin HNP4.
ComponentsNeutrophil defensin 4
KeywordsANTIMICROBIAL PROTEIN / HUMAN ALPHA-DEFENSIN / ANTIMICROBIAL PEPTIDE
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / Defensins / antifungal humoral response / antimicrobial humoral response / Alpha-defensins / azurophil granule / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi lumen ...disruption of plasma membrane integrity in another organism / Defensins / antifungal humoral response / antimicrobial humoral response / Alpha-defensins / azurophil granule / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi lumen / specific granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / protein homodimerization activity / extracellular space / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsGohain, N. / Tolbert, W.D. / Pazgier, M.
CitationJournal: Biochim Biophys Acta Biomembr / Year: 2019
Title: Systematic mutational analysis of human neutrophil alpha-defensin HNP4.
Authors: Hu, H. / Di, B. / Tolbert, W.D. / Gohain, N. / Yuan, W. / Gao, P. / Ma, B. / He, Q. / Pazgier, M. / Zhao, L. / Lu, W.
History
DepositionJun 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 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 4
B: Neutrophil defensin 4
C: Neutrophil defensin 4
D: Neutrophil defensin 4
E: Neutrophil defensin 4
F: Neutrophil defensin 4
G: Neutrophil defensin 4
H: Neutrophil defensin 4
I: Neutrophil defensin 4
J: Neutrophil defensin 4
K: Neutrophil defensin 4
L: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,16436
Polymers44,81412
Non-polymers2,35024
Water5,116284
1
A: Neutrophil defensin 4
B: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,7795
Polymers7,4692
Non-polymers3103
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Neutrophil defensin 4
D: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6614
Polymers7,4692
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Neutrophil defensin 4
F: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6614
Polymers7,4692
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Neutrophil defensin 4
H: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9497
Polymers7,4692
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
I: Neutrophil defensin 4
J: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9717
Polymers7,4692
Non-polymers5025
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
K: Neutrophil defensin 4
L: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,1419
Polymers7,4692
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.629, 65.894, 124.064
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide
Neutrophil defensin 4 / Defensin / alpha 4 / HNP-4 / HP-4


Mass: 3734.512 Da / Num. of mol.: 12 / Mutation: G23A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P12838
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 1.9 Å3/Da / Density % sol: 35.21 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% isopropanol 10% PEG 1500 200 mM lithium sulfate 100 mM sodium acetate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2016
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 40384 / % possible obs: 99.8 % / Redundancy: 4.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.031 / Net I/σ(I): 28.8
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.966 / Num. unique all: 1991 / CC1/2: 0.71 / Rpim(I) all: 0.521 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZMM

1zmm


Resolution: 1.67→34.567 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.5 / Phase error: 28.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2531 2011 5.02 %
Rwork0.218 --
obs0.2198 40053 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.67→34.567 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2964 0 126 284 3374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113148
X-RAY DIFFRACTIONf_angle_d1.324271
X-RAY DIFFRACTIONf_dihedral_angle_d10.7791971
X-RAY DIFFRACTIONf_chiral_restr0.062502
X-RAY DIFFRACTIONf_plane_restr0.006498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6699-1.71170.37591420.35582600X-RAY DIFFRACTION97
1.7117-1.7580.34791390.31752717X-RAY DIFFRACTION100
1.758-1.80970.30651620.2852716X-RAY DIFFRACTION100
1.8097-1.86810.31361300.25362671X-RAY DIFFRACTION100
1.8681-1.93490.29781440.24072677X-RAY DIFFRACTION99
1.9349-2.01230.27521180.24252726X-RAY DIFFRACTION99
2.0123-2.10390.23271540.22082692X-RAY DIFFRACTION99
2.1039-2.21480.24851330.20692715X-RAY DIFFRACTION99
2.2148-2.35350.23611330.21382728X-RAY DIFFRACTION99
2.3535-2.53520.28011430.21952713X-RAY DIFFRACTION99
2.5352-2.79020.29941500.22182724X-RAY DIFFRACTION99
2.7902-3.19370.23141630.2012733X-RAY DIFFRACTION99
3.1937-4.02280.21731510.18212761X-RAY DIFFRACTION99
4.0228-34.57410.23521490.2152869X-RAY DIFFRACTION97
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)
14.3274-0.7998-2.6254.82350.22134.09730.12070.279-0.1557-0.3619-0.03430.4994-0.0971-0.1613-0.08540.16010.0016-0.07950.20090.02640.2137-11.27766.707626.0965
21.9612.0695-0.31337.11552.86412.144100.0056-0.1090.0732-0.0541-0.11730.06440.0430.00890.17970.0066-0.06740.240.03170.235-15.4579-6.841831.6654
32.1355-1.57173.32276.8637-0.44996.0923-0.04040.01340.03660.12130.0768-0.3240.03660.13980.01620.11120.01480.03070.19860.00130.2912-9.2099-6.85355.6059
44.58313.9354-1.55374.23370.24075.172-0.25840.0441-0.0676-0.3580.17540.1492-0.357-0.23430.09420.29070.09870.00830.25120.03630.27-4.90126.423511.492
57.72240.05523.82054.8752-0.21166.1034-0.07640.1040.0965-0.19830.0729-0.09610.03610.03690.02880.1735-0.0010.01050.15530.01780.1162-9.4665-7.028946.2722
68.14384.2166-2.81666.626-2.86216.14890.1045-0.35190.07060.0261-0.06910.0888-0.1091-0.0389-0.00240.27540.0276-0.04330.2183-0.04610.2341-4.80386.320452.063
75.46181.9397-0.18277.68441.57565.6621-0.14580.3333-0.0528-1.15860.3322-0.6025-1.050.22-0.18660.4124-0.05030.07670.2259-0.03810.1889-31.4716.651455.6365
86.027-0.2266-0.25313.1001-1.56146.7554-0.1368-0.4518-0.43830.74070.17860.15020.8757-0.0142-0.03990.5113-0.00060.0070.22830.01350.1727-27.1765-6.963651.8608
97.24592.28532.11919.73431.89166.7387-0.19660.5568-0.2688-0.92110.4281-0.7476-0.8540.5197-0.22010.2662-0.01960.07160.2368-0.03710.1922-30.95317.003314.0784
106.785-1.6619-0.13999.4266-0.18987.5316-0.0934-0.4278-0.38180.46170.2409-0.06520.3308-0.1225-0.13250.14710.02980.01030.26860.02130.1526-26.7854-7.12710.5622
118.97323.23080.89199.4749-0.17674.4580.13960.1513-0.00370.33490.0740.43880.2685-0.1676-0.1460.1382-0.0047-0.00370.16730.01430.1006-30.8392-7.490734.636
125.8444-1.6649-0.23458.16661.0645.7449-0.1688-0.41690.55160.66890.3296-0.1563-0.3904-0.088-0.14060.17550.0578-0.01140.23360.00270.1965-34.71176.601131.037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 33)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 31)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 33)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 31)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 33)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 31)
7X-RAY DIFFRACTION7(chain 'G' and resid 1 through 31)
8X-RAY DIFFRACTION8(chain 'H' and resid 1 through 32)
9X-RAY DIFFRACTION9(chain 'I' and resid 1 through 32)
10X-RAY DIFFRACTION10(chain 'J' and resid 1 through 33)
11X-RAY DIFFRACTION11(chain 'K' and resid 1 through 32)
12X-RAY DIFFRACTION12(chain 'L' and resid 1 through 32)

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