[English] 日本語
Yorodumi
- PDB-3i5w: Crystal structure of human alpha-defensin 5 (mutant R13H) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3i5w
TitleCrystal structure of human alpha-defensin 5 (mutant R13H)
ComponentsDefensin-5
KeywordsANTIMICROBIAL PROTEIN / human alpha-defensin 5 / HD5 / antimicrobial peptide / Antibiotic / Antimicrobial / Defensin / Disulfide bond / Fungicide / Secreted
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 / antibacterial humoral response / midbody / cellular response to lipopolysaccharide / secretory granule lumen / protein homotetramerization / defense response to Gram-negative bacterium / 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 / Defensin propeptide / Alpha-defensin propeptide / Alpha-defensin / Defensin propeptide / Beta/alpha-defensin, C-terminal / Defensin/corticostatin family
Similarity search - Domain/homology
CITRATE ANION / Defensin alpha 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsPazgier, M. / Lu, W.
CitationJournal: Febs Lett. / Year: 2009
Title: Selective arginines are important for the antibacterial activity and host cell interaction of human alpha-defensin 5
Authors: de Leeuw, E. / Rajabi, M. / Zou, G. / Pazgier, M. / Lu, W.
History
DepositionJul 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Refinement description / Version format compliance
Revision 1.2Apr 11, 2012Group: Derived calculations
Revision 1.3Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.4Oct 27, 2021Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific
Revision 1.5Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)7,3754
Polymers7,1502
Non-polymers2252
Water1,17165
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-5 kcal/mol
Surface area4490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.018, 49.754, 62.355
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-33-

CL

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 6 / Auth seq-ID: 1 - 32 / Label seq-ID: 1 - 32

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

-
Components

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


Mass: 3575.181 Da / Num. of mol.: 2 / Mutation: R13H / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q01523
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 65 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% PEG 4000, 20% 2-propanol, 0.1M Na citrate buffer, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 273K

-
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 15, 2009 / Details: confocal
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.63→38.891 Å / Num. all: 9653 / Num. obs: 9433 / % possible obs: 97.7 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.7
Reflection shellResolution: 1.63→1.66 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 3.4 / Num. unique all: 399 / % possible all: 81.6

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0070refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1ZMP

1zmp


Resolution: 1.63→20 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.092 / SU ML: 0.05 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.086 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.194 456 4.8 %RANDOM
Rwork0.176 ---
obs0.177 9429 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.81 Å2 / Biso mean: 28.288 Å2 / Biso min: 18.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.79 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.63→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms488 0 14 65 567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.021518
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.995701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.546566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.4971720
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5341588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9171510
X-RAY DIFFRACTIONr_chiral_restr0.1190.277
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02386
X-RAY DIFFRACTIONr_mcbond_it1.2081.5322
X-RAY DIFFRACTIONr_mcangle_it2.0212515
X-RAY DIFFRACTIONr_scbond_it3.0383196
X-RAY DIFFRACTIONr_scangle_it5.2724.5184
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 238 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.625
LOOSE THERMAL3.3510
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.198 30 -
Rwork0.263 609 -
all-639 -
obs--90.9 %
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)
13.85020.01050.292.24940.26842.8170.04750.032-0.19550.02660.0528-0.06620.21910.1177-0.10030.04560.0132-0.01190.0101-0.00020.02522.118-7.77811.0245
21.45021.8323-1.89563.9555-2.1642.5411-0.14290.1125-0.0472-0.27780.0958-0.01580.1168-0.12780.04710.0947-0.03570.00290.08010.00010.0823-10.1341-13.31569.7572
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 32
2X-RAY DIFFRACTION1A33
3X-RAY DIFFRACTION1A34 - 66
4X-RAY DIFFRACTION2B1 - 32
5X-RAY DIFFRACTION2B33
6X-RAY DIFFRACTION2B34 - 65

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlc1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more