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- PDB-4rbw: Crystal structure of human alpha-defensin 5, HD5 (Thr7Arg Glu21Ar... -

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Basic information

Entry
Database: PDB / ID: 4rbw
TitleCrystal structure of human alpha-defensin 5, HD5 (Thr7Arg Glu21Arg mutant)
ComponentsDefensin-5
KeywordsANTIMICROBIAL PROTEIN / MUTANT T7R E21R-HD5 / BETA-SHEET / ANTIMICROBIAL PEPTIDE / PANETH CELLS DEFENSIN / HUMAN ALPHA-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: 1.5 Å
AuthorsPazgier, M. / Gohain, N. / Tolbert, W.D.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Design of a potent antibiotic peptide based on the active region of human defensin 5.
Authors: Wang, C. / Shen, M. / Gohain, N. / Tolbert, W.D. / Chen, F. / Zhang, N. / Yang, K. / Wang, A. / Su, Y. / Cheng, T. / Zhao, J. / Pazgier, M. / Wang, J.
History
DepositionSep 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,64915
Polymers14,7144
Non-polymers93511
Water1,35175
1
A: Defensin-5
D: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8377
Polymers7,3572
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-60 kcal/mol
Surface area4920 Å2
MethodPISA
2
B: Defensin-5
C: Defensin-5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,8128
Polymers7,3572
Non-polymers4556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-41 kcal/mol
Surface area4910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)20.550, 51.703, 50.676
Angle α, β, γ (deg.)90.00, 96.35, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide
Defensin-5 / / HD5(63-94)


Mass: 3678.398 Da / Num. of mol.: 4 / Mutation: T7R, E21R / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01523
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 1.82 Å3/Da / Density % sol: 32.36 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES pH 6.5, 0.5M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2014
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.5→36.08 Å / Num. all: 16958 / Num. obs: 15346 / % possible obs: 90.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 28.6
Reflection shellResolution: 1.5→1.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.8 / % possible all: 93.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZMP

1zmp


Resolution: 1.5→36.077 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.978 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22131 766 5 %RANDOM
Rwork0.18205 ---
obs0.1841 14565 90.46 %-
all-16081 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20.1 Å2
2--1 Å2-0 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.077 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 47 75 1122
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191091
X-RAY DIFFRACTIONr_bond_other_d0.0010.021040
X-RAY DIFFRACTIONr_angle_refined_deg2.072.0121463
X-RAY DIFFRACTIONr_angle_other_deg0.87132349
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5415132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg11.69113.40447
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94515203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4131535
X-RAY DIFFRACTIONr_chiral_restr0.120.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021165
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02302
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_it2.1972.062522
X-RAY DIFFRACTIONr_mcbond_other2.1912.06521
X-RAY DIFFRACTIONr_mcangle_it3.2213.084650
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.0022.527569
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 66 -
Rwork0.194 1060 -
obs--91.54 %
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)
10.397-0.0540.1330.1631-0.13820.4221-0.0148-0.020.0252-0.0226-0.01870.01580.02870.00450.03350.00660.0005-0.00260.0177-0.00310.0097-5.15939.215-1.8898
20.5442-0.1772-0.07730.2061-0.24380.5477-0.01050.0304-0.03340.0187-0.00190.0218-0.0153-0.00410.01240.00690.00070.00480.00900.01684.532711.668315.8996
30.2490.2334-0.07390.51360.43790.89520.0198-0.0094-0.02690.0123-0.0002-0.0452-0.00830.0101-0.01960.00830.001-0.00380.00360.00150.014-3.930413.482425.4542
40.1923-0.1399-0.04250.64950.36960.6290.0001-0.0190.0038-0.00280.0178-0.03760.016-0.0193-0.01790.0080.0012-0.00270.0045-0.00070.0104-13.76216.4117-10.9914
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

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