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- PDB-3qte: Crystal structure of human alpha-defensin 6 (H27W mutant) -

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Basic information

Entry
Database: PDB / ID: 3qte
TitleCrystal structure of human alpha-defensin 6 (H27W mutant)
ComponentsDefensin-6
KeywordsANTIMICROBIAL PROTEIN / Paneth cells defensin / HD6 / human alpha defensin
Function / homology
Function and homology information


disruption of plasma membrane integrity in another organism / Defensins / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide ...disruption of plasma membrane integrity in another organism / Defensins / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / Golgi 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 / 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 / MOLECULAR REPLACEMENT / Resolution: 1.949 Å
AuthorsPazgier, M. / Lu, W.
CitationJournal: Science / Year: 2012
Title: Human alpha-defensin 6 promotes mucosal innate immunity through self-assembled peptide nanonets.
Authors: Chu, H. / Pazgier, M. / Jung, G. / Nuccio, S.P. / Castillo, P.A. / de Jong, M.F. / Winter, M.G. / Winter, S.E. / Wehkamp, J. / Shen, B. / Salzman, N.H. / Underwood, M.A. / Tsolis, R.M. / ...Authors: Chu, H. / Pazgier, M. / Jung, G. / Nuccio, S.P. / Castillo, P.A. / de Jong, M.F. / Winter, M.G. / Winter, S.E. / Wehkamp, J. / Shen, B. / Salzman, N.H. / Underwood, M.A. / Tsolis, R.M. / Young, G.M. / Lu, W. / Lehrer, R.I. / Baumler, A.J. / Bevins, C.L.
History
DepositionFeb 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 13, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin-6
B: Defensin-6
C: Defensin-6
D: Defensin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,2327
Polymers15,0694
Non-polymers1633
Water70339
1
A: Defensin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8032
Polymers3,7671
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Defensin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8032
Polymers3,7671
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Defensin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8592
Polymers3,7671
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Defensin-6


Theoretical massNumber of molelcules
Total (without water)3,7671
Polymers3,7671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Defensin-6
B: Defensin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6064
Polymers7,5352
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area770 Å2
ΔGint-17 kcal/mol
Surface area5100 Å2
MethodPISA
6
C: Defensin-6
hetero molecules

D: Defensin-6


Theoretical massNumber of molelcules
Total (without water)7,6273
Polymers7,5352
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area610 Å2
ΔGint-16 kcal/mol
Surface area5100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.774, 32.675, 54.005
Angle α, β, γ (deg.)90.00, 108.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Defensin-6 / Defensin / alpha 6


Mass: 3767.367 Da / Num. of mol.: 4 / Fragment: Processed peptide (UNP Residues 69-100) / Mutation: H95W / Source method: obtained synthetically / Details: This sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01524
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.88 Å3/Da / Density % sol: 34.47 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M imidazole, pH 6.5, 1M Na acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.949→50 Å / Num. all: 8330 / Num. obs: 8258 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.7 % / Rmerge(I) obs: 0.105 / Rsym value: 0.088 / Net I/σ(I): 16.5
Reflection shellResolution: 1.949→1.98 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.504 / % possible all: 92

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZMQ

1zmq


Resolution: 1.949→20 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / SU B: 8.611 / SU ML: 0.101 / SU R Cruickshank DPI: 0.0449 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.24665 384 4.7 %RANDOM
Rwork0.19243 ---
obs0.19487 7856 98.68 %-
all-8330 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.237 Å2
Baniso -1Baniso -2Baniso -3
1-5.85 Å20 Å233.81 Å2
2---14.83 Å20 Å2
3---8.98 Å2
Refinement stepCycle: LAST / Resolution: 1.949→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 8 39 1083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211081
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8161.9021465
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9235124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.09719.16748
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.87115160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8441512
X-RAY DIFFRACTIONr_chiral_restr0.1210.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02820
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_it0.9981.5632
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.83921016
X-RAY DIFFRACTIONr_scbond_it2.8383449
X-RAY DIFFRACTIONr_scangle_it4.3524.5449
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 23 -
Rwork0.245 494 -
obs--85.6 %
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)
10.62450.6643-0.37282.3162-0.54760.3755-0.03450.0566-0.12770.05940.0080.0391-0.0313-0.09710.02640.09180.0088-0.04880.07880.00390.1305-14.2025-6.5237-5.8372
21.02811.361-0.25221.9313-0.77081.73530.07930.0984-0.12520.02980.0962-0.13880.107-0.034-0.17560.14270.10750.04580.09260.04370.0992-17.85559.6511-16.2589
30.45380.6111-0.72112.4285-0.22571.4974-0.01830.035-0.0252-0.0717-0.04030.05180.0157-0.10860.05860.0695-0.0105-0.08050.0815-0.00140.1157-31.006711.4145-5.9499
41.9801-0.62851.1791.1509-1.51662.2731-0.01110.1973-0.0566-0.0518-0.0589-0.1373-0.0007-0.030.070.08650.0364-0.01270.12450.0370.0996-34.6746-6.2572-16.9398
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION1A34 - 48
3X-RAY DIFFRACTION2B1 - 32
4X-RAY DIFFRACTION2B34 - 38
5X-RAY DIFFRACTION3C1 - 32
6X-RAY DIFFRACTION3C34 - 43
7X-RAY DIFFRACTION4D1 - 32
8X-RAY DIFFRACTION4D33 - 42

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