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- PDB-4e82: Crystal structure of monomeric variant of human alpha-defensin 5,... -

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Basic information

Entry
Database: PDB / ID: 4.0E+82
TitleCrystal structure of monomeric variant of human alpha-defensin 5, HD5 (Glu21EMe mutant)
ComponentsDefensin-5
KeywordsANTIMICROBIAL PROTEIN / monomeric variant / antimicrobial peptide / Glu21 methylation / 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: 1.7 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Defensin-5
B: Defensin-5


Theoretical massNumber of molelcules
Total (without water)7,2172
Polymers7,2172
Non-polymers00
Water99155
1
A: Defensin-5


Theoretical massNumber of molelcules
Total (without water)3,6081
Polymers3,6081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Defensin-5


Theoretical massNumber of molelcules
Total (without water)3,6081
Polymers3,6081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)22.317, 37.733, 59.852
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALACYSCYSAA1 - 201 - 20
21ALAALACYSCYSBB1 - 201 - 20
12ILEILEARGARGAA22 - 3222 - 32
22ILEILEARGARGBB22 - 3222 - 32

NCS ensembles :
ID
1
2

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Components

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


Mass: 3608.255 Da / Num. of mol.: 2 / Fragment: UNP residues 63-94 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01523
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 1.75 Å3/Da / Density % sol: 29.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M sodium citrate tribasic dehydrate, 0.1 M HEPES sodium, 20% isopropanol, pH 7.5, 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: Jun 17, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 11157 / Num. obs: 6204 / % possible obs: 56 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Rmerge(I) obs: 0.122 / Rsym value: 0.165 / Net I/σ(I): 17.5
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 3.8 / Rsym value: 0.18 / % possible all: 92.3

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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: 1.7→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.946 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.091 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2124 265 4.6 %RANDOM
Rwork0.1702 ---
obs0.1721 5743 96.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.97 Å2 / Biso mean: 26.7686 Å2 / Biso min: 15.13 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms492 0 0 55 547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019496
X-RAY DIFFRACTIONr_angle_refined_deg1.8052.009658
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.321558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.35414.44418
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6841586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0981512
X-RAY DIFFRACTIONr_chiral_restr0.1110.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRms dev position (Å)Weight position
11A18X-RAY DIFFRACTION0.110.05
12B18X-RAY DIFFRACTION0.110.05
21A10X-RAY DIFFRACTION0.090.05
22B10X-RAY DIFFRACTION0.090.05
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 15 -
Rwork0.195 332 -
all-347 -
obs--95.33 %
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)
11.9117-0.03710.13233.652-1.5453.1511-0.0376-0.0210.08810.05820.004-0.0017-0.19680.02380.03360.02290.0059-0.00640.0113-0.00110.0073-11.17362.03838.5443
22.20.19780.33712.19631.31132.4292-0.0511-0.0686-0.06510.08610.0706-0.0540.04040.0591-0.01950.01690.0117-0.00540.02310.00290.0071-1.6044-7.25889.1583
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2B1 - 32

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