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- PDB-5cuj: Crystal structure of Human Defensin-5 Y27A mutant crystal form 2. -

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Basic information

Entry
Database: PDB / ID: 5cuj
TitleCrystal structure of Human Defensin-5 Y27A mutant crystal form 2.
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 ...citation / citation_author / pdbx_struct_oper_list / pdbx_struct_special_symmetry
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.pdbx_dist_value / _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

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)21,87323
Polymers21,0136
Non-polymers86017
Water1,20767
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-154 kcal/mol
Surface area10630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.758, 59.758, 47.284
Angle α, β, γ (deg.)90.00, 105.54, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-103-

CL

21B-102-

CL

31F-101-

CL

41C-215-

HOH

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Components

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


Mass: 3502.132 Da / Num. of mol.: 6 / 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.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


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


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3 M sodium chloride, 5% MPD, 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: BL12-2 / Wavelength: 0.9795 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2015 / Details: Rh coated mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. all: 11584 / Num. obs: 11584 / % possible obs: 97.4 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 11
Reflection shellResolution: 2.08→2.13 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 1.1 / % possible all: 92.3

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Processing

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

1zmp


Resolution: 2.08→45.74 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.905 / SU B: 16.135 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29206 582 5 %RANDOM
Rwork0.23454 ---
obs0.23729 10420 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.198 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å22.11 Å2
2---0.54 Å2-0 Å2
3---0.57 Å2
Refinement stepCycle: 1 / Resolution: 2.08→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1428 0 38 67 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191467
X-RAY DIFFRACTIONr_bond_other_d0.0020.021425
X-RAY DIFFRACTIONr_angle_refined_deg1.1092.0041968
X-RAY DIFFRACTIONr_angle_other_deg0.80633237
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9725186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.91415.55654
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39515264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8271536
X-RAY DIFFRACTIONr_chiral_restr0.0540.2228
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021602
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02354
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_it0.3523.54762
X-RAY DIFFRACTIONr_mcbond_other0.3523.539761
X-RAY DIFFRACTIONr_mcangle_it0.615.305942
X-RAY DIFFRACTIONr_mcangle_other0.615.306943
X-RAY DIFFRACTIONr_scbond_it0.3463.752705
X-RAY DIFFRACTIONr_scbond_other0.3463.76706
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.5865.6111027
X-RAY DIFFRACTIONr_long_range_B_refined2.90133.3945267
X-RAY DIFFRACTIONr_long_range_B_other2.6733.3275237
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.085→2.139 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 46 -
Rwork0.332 745 -
obs--89.58 %
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)
18.281-1.1052-0.2396.9712-1.18146.50470.1307-0.41340.1351-0.4699-0.18930.1283-0.3530.01460.05860.12230.03330.05930.1406-0.0180.102715.73366.33418.0953
22.8489-0.29310.58646.41370.03335.40770.0095-0.5117-0.10310.12680.22620.05370.140.0929-0.23570.0138-0.00780.01730.30350.00760.085424.2372-5.263122.5568
37.7026-1.24881.5166.52480.96385.697-0.02570.31850.35080.17420.0730.2123-0.3516-0.0644-0.04730.07080.05050.08270.06360.08610.140614.04875.79843.333
44.1711.83731.08035.018-0.81786.8517-0.13120.1003-0.1893-0.1569-0.14360.23070.2102-0.31790.27480.0326-0.02480.06550.0588-0.08820.21214.7254-18.59344.5779
55.5551.3266-1.01955.11821.56416.7659-0.113-0.346-0.14230.602-0.1387-0.01410.03020.2920.25160.1214-0.03380.05260.18980.03950.157216.5684-17.68619.5871
65.1548-0.2221-0.07758.021-1.97743.66770.23040.3634-0.2335-0.17450.1440.16650.1509-0.3256-0.37440.0230.00430.00520.1991-0.01470.24286.3378-6.83640.2984
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION2B1 - 32
3X-RAY DIFFRACTION3C1 - 32
4X-RAY DIFFRACTION4D1 - 32
5X-RAY DIFFRACTION5E1 - 32
6X-RAY DIFFRACTION6F1 - 32

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