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- PDB-5cum: Crystal structure of Human Defensin-5 Y27A mutant crystal form 1. -

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Basic information

Entry
Database: PDB / ID: 5cum
TitleCrystal structure of Human Defensin-5 Y27A mutant crystal form 1.
ComponentsDefensin-5
KeywordsANTIMICROBIAL PROTEIN / PANETH CELLS DEFENSIN / HUMAN ALPHA-DEFENSIN / INTESTINAL DEFENSIN
Function / homology
Function and homology information


positive regulation of membrane permeability / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / secretory granule / positive regulation of interleukin-8 production ...positive regulation of membrane permeability / Defensins / disruption of plasma membrane integrity in another organism / killing by host of symbiont cells / Alpha-defensins / defense response to fungus / transport vesicle / innate immune response in mucosa / secretory granule / positive regulation of interleukin-8 production / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / midbody / antibacterial humoral response / protein homotetramerization / secretory granule lumen / killing of cells of another organism / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / 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 / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Defensin alpha 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.752 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 ...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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Defensin-5
B: Defensin-5
C: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,93913
Polymers10,5063
Non-polymers43310
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-61 kcal/mol
Surface area7130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.603, 59.966, 38.272
Angle α, β, γ (deg.)90.00, 111.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-102-

CL

21A-103-

CL

31B-208-

HOH

41B-223-

HOH

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Components

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


Mass: 3502.132 Da / Num. of mol.: 3 / Mutation: Y27A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01523
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.429 M sodium chloride, 9.9% isopropanol, 0.1 M calcium chloride, and 0.1 M imidazole pH 6.5
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 23, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 10121 / Num. obs: 10121 / % possible obs: 99.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.2
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.704 / Mean I/σ(I) obs: 1.2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
REFMAC5.8refinement
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZMP

1zmp


Resolution: 1.752→35.649 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2196 477 4.68 %
Rwork0.1726 --
obs0.1749 10119 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.752→35.649 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms714 0 19 79 812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008732
X-RAY DIFFRACTIONf_angle_d1.231960
X-RAY DIFFRACTIONf_dihedral_angle_d11.41276
X-RAY DIFFRACTIONf_chiral_restr0.052111
X-RAY DIFFRACTIONf_plane_restr0.005123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7518-1.84420.36411090.25992735X-RAY DIFFRACTION100
1.8442-1.95970.24461310.21452664X-RAY DIFFRACTION100
1.9597-2.1110.2324970.19682769X-RAY DIFFRACTION100
2.111-2.32340.21641750.15992609X-RAY DIFFRACTION100
2.3234-2.65950.18321010.17782772X-RAY DIFFRACTION100
2.6595-3.35030.23021910.17582617X-RAY DIFFRACTION100
3.3503-35.65620.2051240.14972717X-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)
19.2443-1.9879-1.30979.16990.58568.44280.03530.4687-0.0291-0.26320.0968-0.3528-0.01760.9593-0.12550.1954-0.03160.01580.3128-0.01110.1042113.47-21.993324.0931
28.3875-0.41770.83148.83570.71946.0199-0.4349-0.31490.62980.36890.1958-0.0538-0.6673-0.37960.25210.2180.0954-0.0460.2028-0.01620.236398.0104-10.182638.6698
37.36792.2402-0.76849.5535-1.72989.2290.3466-0.4753-0.7060.2698-0.12740.06020.4753-0.2897-0.22740.186-0.0705-0.06010.16740.01950.281198.2783-34.580938.4342
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)

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