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- PDB-4e83: Crystal structure of human alpha-defensin 5, HD5 (Leu29NLe mutant) -

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Basic information

Entry
Database: PDB / ID: 4.0E+83
TitleCrystal structure of human alpha-defensin 5, HD5 (Leu29NLe mutant)
ComponentsDefensin-5
KeywordsANTIMICROBIAL PROTEIN / beta-sheet structure / antimicrobial peptide / Leu29Nle mutant / Paneth cells
Function / homology
Function and homology information


positive regulation of membrane permeability / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / Alpha-defensins / Mitochondrial unfolded protein response (UPRmt) / defense response to fungus / transport vesicle / secretory granule / innate immune response in mucosa ...positive regulation of membrane permeability / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / Alpha-defensins / Mitochondrial unfolded protein response (UPRmt) / defense response to fungus / transport vesicle / secretory granule / innate immune response in mucosa / positive regulation of interleukin-8 production / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / midbody / secretory granule lumen / defense response to Gram-negative bacterium / protein homotetramerization / killing of cells of another organism / defense response to Gram-positive bacterium / innate immune response / intracellular membrane-bounded organelle / 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: 1.9 Å
AuthorsPazgier, M.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Functional determinants of human enteric {alpha}-defensin HD5: crucial role for hydrophobicity at dimer interface.
Authors: Rajabi, M. / Ericksen, B. / Wu, X. / de Leeuw, E. / Zhao, L. / Pazgier, M. / Lu, W.
History
DepositionMar 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: 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_conn / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 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: Defensin-5
B: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,2243
Polymers7,1882
Non-polymers351
Water43224
1
A: Defensin-5


Theoretical massNumber of molelcules
Total (without water)3,5941
Polymers3,5941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,6302
Polymers3,5941
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-9 kcal/mol
Surface area4580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.229, 60.772, 20.392
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-101-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: 1 - 32 / Label seq-ID: 1 - 32

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein/peptide Defensin-5 / alpha-defensin 5 / HD5 / Defensin / alpha 5


Mass: 3594.228 Da / Num. of mol.: 2 / Fragment: UNP residues 63-94 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01523
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.69 Å3/Da / Density % sol: 27.25 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.0 M HEPES sodium, pH 7.5, 0.2 M magnesium chloride hexahydrate, 30% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Sep 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.81→50 Å / Num. all: 8069 / Num. obs: 4623 / % possible obs: 57 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 5.9 % / Rmerge(I) obs: 0.081 / Rsym value: 0.057 / Net I/σ(I): 21
Reflection shellResolution: 1.81→1.84 Å / Redundancy: 3 % / Rmerge(I) obs: 0.406 / Mean I/σ(I) obs: 1.2 / Rsym value: 0.362 / % possible all: 66.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZMP

1zmp


Resolution: 1.9→32.96 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.897 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2429 193 4.6 %RANDOM
Rwork0.1988 ---
obs0.201 4153 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 96.34 Å2 / Biso mean: 51.818 Å2 / Biso min: 24.01 Å2
Baniso -1Baniso -2Baniso -3
1--2.63 Å20 Å20 Å2
2--3.32 Å20 Å2
3----0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.9→32.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms490 0 1 24 515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.019498
X-RAY DIFFRACTIONr_angle_refined_deg1.9971.993666
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.149562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.1291620
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.9641586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2781512
X-RAY DIFFRACTIONr_chiral_restr0.1140.272
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02364
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A33X-RAY DIFFRACTION0.180.05
12B33X-RAY DIFFRACTION0.180.05
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 8 -
Rwork0.293 241 -
all-249 -
obs--94.68 %
Refinement TLS params.Method: refined / Origin x: 0.634 Å / Origin y: 11.456 Å / Origin z: -0.214 Å
111213212223313233
T0.1793 Å20.0052 Å2-0.0035 Å2-0.0516 Å20.0137 Å2--0.1419 Å2
L2.6367 °21.3728 °20.7366 °2-1.9981 °20.9561 °2--1.4065 °2
S-0.0111 Å °0.0275 Å °0.1473 Å °-0.0134 Å °-0.0398 Å °0.1362 Å °0.0379 Å °0.0943 Å °0.0509 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION1A101 - 109
3X-RAY DIFFRACTION1B1 - 32
4X-RAY DIFFRACTION1B101
5X-RAY DIFFRACTION1B201 - 215

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