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- PDB-5cui: Crystal structure of Human Defensin-5 R28A mutant. -

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Basic information

Entry
Database: PDB / ID: 5cui
TitleCrystal structure of Human Defensin-5 R28A mutant.
ComponentsDefensin-5
KeywordsANTIMICROBIAL PROTEIN / PANETH CELLS DEFENSIN / HUMAN ALPHA-DEFENSIN / INTESTINAL DEFENSIN
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 / defense response to fungus / transport vesicle / secretory granule / innate immune response in mucosa / positive regulation of interleukin-8 production ...positive regulation of membrane permeability / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / Alpha-defensins / 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 / midbody / cellular response to lipopolysaccharide / secretory granule lumen / defense response to Gram-negative bacterium / protein homotetramerization / killing of cells of another organism / defense response to Gram-positive bacterium / intracellular membrane-bounded organelle / innate immune response / 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: 2.403 Å
AuthorsTolbert, W.D. / Gohain, N. / Pazgier, M.
CitationJournal: Immunity / Year: 2018
Title: Human Enteric alpha-Defensin 5 Promotes Shigella Infection by Enhancing Bacterial Adhesion and Invasion.
Authors: Xu, D. / Liao, C. / Zhang, B. / Tolbert, W.D. / He, W. / Dai, Z. / Zhang, W. / Yuan, W. / Pazgier, M. / Liu, J. / Yu, J. / Sansonetti, P.J. / Bevins, C.L. / Shao, Y. / Lu, W.
History
DepositionJul 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 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-5
B: Defensin-5
C: Defensin-5
D: Defensin-5
E: Defensin-5
F: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,51225
Polymers21,0496
Non-polymers1,46319
Water1,26170
1
A: Defensin-5
B: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4817
Polymers7,0162
Non-polymers4655
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Defensin-5
D: Defensin-5
E: Defensin-5
F: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,03118
Polymers14,0324
Non-polymers99914
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9010 Å2
ΔGint-140 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 103.745, 103.985
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-101-

CL

21D-101-

CL

31E-101-

CL

41F-101-

CL

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Components

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Protein/peptide , 1 types, 6 molecules ABCDEF

#1: Protein/peptide
Defensin-5 / Defensin / alpha 5 / HD5(20-94)


Mass: 3508.112 Da / Num. of mol.: 6 / Mutation: R28A / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01523

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Non-polymers , 5 types, 89 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PG0 / 2-(2-METHOXYETHOXY)ETHANOL / PEG 6000


Mass: 120.147 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O3 / Comment: inhibitor, precipitant*YM
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


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


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.85 Å3/Da / Density % sol: 68.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 2.5 M sodium chloride, 12% PEG 1500, 1.5% MPD, and 0.1M sodium acetate pH 5.5
PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 12932 / Num. obs: 12932 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.152 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.903 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
REFMAC5.8.0124refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZMP

1zmp


Resolution: 2.403→36.732 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.221 1236 5.08 %
Rwork0.1829 --
obs0.1848 12930 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.403→36.732 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 83 70 1587
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091522
X-RAY DIFFRACTIONf_angle_d1.0711994
X-RAY DIFFRACTIONf_dihedral_angle_d12.208564
X-RAY DIFFRACTIONf_chiral_restr0.036225
X-RAY DIFFRACTIONf_plane_restr0.003246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4031-2.49930.2941180.22492531X-RAY DIFFRACTION99
2.4993-2.6130.25791440.21452544X-RAY DIFFRACTION100
2.613-2.75070.24481560.19642539X-RAY DIFFRACTION100
2.7507-2.9230.24961770.19522535X-RAY DIFFRACTION100
2.923-3.14850.21391290.16892619X-RAY DIFFRACTION100
3.1485-3.46520.2741170.15982548X-RAY DIFFRACTION100
3.4652-3.96610.17861520.15942601X-RAY DIFFRACTION100
3.9661-4.99480.17051230.15382583X-RAY DIFFRACTION100
4.9948-36.73590.26441200.23892572X-RAY DIFFRACTION100
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)
16.2312-4.5474-3.35638.77110.01579.6634-0.1042-0.42260.1260.31310.28210.08260.16520.19-0.12950.18940.071-0.00480.4238-0.04390.3155-9.046823.1846151.5549
25.91382.4644-0.66615.08821.76847.40750.0240.36240.1213-0.31160.063-0.3843-0.25140.48160.00530.22570.00230.03360.2943-0.0670.31680.721623.4224142.7324
39.4711-0.76631.22469.61841.23463.89020.1704-0.49950.23550.3619-0.235-0.4631-0.089-0.08730.07740.2774-0.02160.05620.3043-0.05660.27875.776214.8539134.4898
43.9948-1.07930.07968.27282.64718.0061-0.18610.2156-0.0539-0.33380.14350.17160.0925-0.0410.02630.4061-0.07260.02330.23380.00070.30290.59276.4865125.7017
57.67334.72680.54784.92681.84945.28180.3392-0.39060.25920.2821-0.1637-0.1845-0.02270.046-0.12440.3142-0.1070.00090.32360.00850.27099.629822.2388116.9035
65.3060.05380.6148.0429-0.07895.4826-0.08510.3611-0.3047-0.4079-0.0271-0.15340.3028-0.02630.09730.3278-0.0025-0.07760.31710.0250.34335.02613.6327108.0503
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 32)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 32)
3X-RAY DIFFRACTION3(chain 'C' and resid 1 through 32)
4X-RAY DIFFRACTION4(chain 'D' and resid 1 through 32)
5X-RAY DIFFRACTION5(chain 'E' and resid 1 through 32)
6X-RAY DIFFRACTION6(chain 'F' and resid 1 through 32)

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