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- PDB-6dmq: Crystal structure of the T27A mutant of human alpha defensin HNP4. -

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Basic information

Entry
Database: PDB / ID: 6dmq
TitleCrystal structure of the T27A mutant of human alpha defensin HNP4.
ComponentsNeutrophil defensin 4
KeywordsANTIMICROBIAL PROTEIN / HUMAN ALPHA-DEFENSIN / ANTIMICROBIAL PEPTIDE
Function / homology
Function and homology information


Defensins / disruption of plasma membrane integrity in another organism / antifungal humoral response / antimicrobial humoral response / Alpha-defensins / azurophil granule / defense response to fungus / transport vesicle / extracellular matrix / innate immune response in mucosa ...Defensins / disruption of plasma membrane integrity in another organism / antifungal humoral response / antimicrobial humoral response / Alpha-defensins / azurophil granule / defense response to fungus / transport vesicle / extracellular matrix / 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 / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / 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: 1.7 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6429
Polymers29,5248
Non-polymers1181
Water3,099172
1
A: Neutrophil defensin 4
B: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)7,3812
Polymers7,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-4 kcal/mol
Surface area4850 Å2
MethodPISA
2
C: Neutrophil defensin 4
D: Neutrophil defensin 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4993
Polymers7,3812
Non-polymers1181
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-12 kcal/mol
Surface area4700 Å2
MethodPISA
3
E: Neutrophil defensin 4
F: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)7,3812
Polymers7,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area640 Å2
ΔGint-5 kcal/mol
Surface area4750 Å2
MethodPISA
4
G: Neutrophil defensin 4
H: Neutrophil defensin 4


Theoretical massNumber of molelcules
Total (without water)7,3812
Polymers7,3812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-5 kcal/mol
Surface area4470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.704, 38.989, 71.130
Angle α, β, γ (deg.)90.00, 108.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 3690.460 Da / Num. of mol.: 8 / Mutation: T27A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P12838
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 30% MPD 15% PEG 8000 100 mM sodium acetate pH 5.5 100 mM calcium chloride

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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: 1.7→50 Å / Num. obs: 27445 / % possible obs: 99.7 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.06 / Net I/σ(I): 17.7
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.67 / Rpim(I) all: 0.66 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZMM

1zmm


Resolution: 1.7→33.73 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.891 / SU B: 2.123 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30998 1383 5 %RANDOM
Rwork0.26909 ---
obs0.27112 26124 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 25.974 Å2
Baniso -1Baniso -2Baniso -3
1-1.88 Å20 Å2-0.13 Å2
2---2.76 Å2-0 Å2
3---0.88 Å2
Refinement stepCycle: 1 / Resolution: 1.7→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1940 0 8 172 2120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0142049
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171816
X-RAY DIFFRACTIONr_angle_refined_deg1.9671.6672768
X-RAY DIFFRACTIONr_angle_other_deg0.9731.6394249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8575259
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.4314.667120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.75115349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7661540
X-RAY DIFFRACTIONr_chiral_restr0.0840.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.022345
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02411
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_it1.2861.6361042
X-RAY DIFFRACTIONr_mcbond_other1.2851.6351041
X-RAY DIFFRACTIONr_mcangle_it1.8892.4431299
X-RAY DIFFRACTIONr_mcangle_other1.8882.4431300
X-RAY DIFFRACTIONr_scbond_it1.4481.8411007
X-RAY DIFFRACTIONr_scbond_other1.4491.8431008
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0762.7141470
X-RAY DIFFRACTIONr_long_range_B_refined4.73719.842117
X-RAY DIFFRACTIONr_long_range_B_other4.7119.5632092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 105 -
Rwork0.179 1870 -
obs--99.55 %
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)
12.2662-1.0948-0.58455.787-0.49333.0667-0.0481-0.2182-0.19650.2609-0.00480.41370.2779-0.12020.05280.0443-0.0180.02130.1132-0.02050.05767.49762.096840.0893
23.3706-0.21140.98863.56830.43383.42860.04260.10340.0552-0.3091-0.05280.22440.0187-0.09040.01010.0280.0006-0.01850.0727-0.00330.020612.9563-2.210426.929
31.777-0.03691.31775.83820.76692.5393-0.0797-0.10070.20450.07760.0421-0.2437-0.24250.19480.03760.0306-0.0272-0.00070.1035-0.01510.0413-5.9748-16.763239.0615
41.1644-0.4106-0.90562.5762-1.93186.10070.00720.0284-0.1423-0.21160.01080.06380.25590.0684-0.01810.0212-0.0106-0.00570.07640.00070.0224-13.5821-11.907527.0309
51.70181.015-0.39755.67030.60662.0006-0.03540.173-0.1766-0.25980.0276-0.4850.24660.15260.00780.05750.02060.02350.12380.010.05244.92862.6016-6.1292
62.50290.38940.90623.3037-0.51144.38320.0055-0.08910.12340.2324-0.0577-0.19710.03350.04840.05220.019-0.0008-0.01370.0751-0.00120.0261-0.6206-2.26296.675
72.0170.33111.06165.8763-0.97642.6037-0.10730.09110.2228-0.08370.08750.1255-0.2174-0.21350.01970.02340.0218-0.00550.09110.01840.029718.314-16.753-5.4556
80.53670.3876-0.65682.26652.09415.55210.0307-0.0221-0.06950.13790.0338-0.06310.1532-0.0078-0.06450.01060.0064-0.00990.06930.00120.023326.2235-11.9396.1771
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2B1 - 32
3X-RAY DIFFRACTION3C1 - 31
4X-RAY DIFFRACTION4D1 - 32
5X-RAY DIFFRACTION5E1 - 31
6X-RAY DIFFRACTION6F1 - 32
7X-RAY DIFFRACTION7G1 - 31
8X-RAY DIFFRACTION8H1 - 31

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