[English] 日本語
Yorodumi
- PDB-4lbf: Crystal structure of HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4lbf
TitleCrystal structure of HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A mutant
ComponentsNeutrophil defensin 1
KeywordsANTIMICROBIAL PROTEIN / ANTIMICROBIAL PEPTIDE / HUMAN ALPHA DEFENSIN 1 / HUMAN NEUTROPHIL PEPTIDE 1 / ANTIBIOTIC / ANTIVIRAL DEFENSE / DEFENSIN / DISULFIDE BOND / FUNGICIDE / PHOSPHOPROTEIN / SECRETED
Function / homology
Function and homology information


pore-forming activity / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa ...pore-forming activity / disruption of plasma membrane integrity in another organism / Defensins / killing by host of symbiont cells / T cell chemotaxis / Alpha-defensins / defense response to protozoan / defense response to fungus / estrogen receptor signaling pathway / innate immune response in mucosa / Golgi lumen / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cellular response to lipopolysaccharide / collagen-containing extracellular matrix / defense response to virus / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / immune response / Neutrophil degranulation / extracellular space / extracellular exosome / 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
Neutrophil defensin 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTolbert, W.D. / Wu, X. / Pazgier, M.
CitationJournal: Plos One / Year: 2013
Title: Single, Double and Quadruple Alanine Substitutions at Oligomeric Interfaces Identify Hydrophobicity as the Key Determinant of Human Neutrophil Alpha Defensin HNP1 Function.
Authors: Zhao, L. / Tolbert, W.D. / Ericksen, B. / Zhan, C. / Wu, X. / Yuan, W. / Li, X. / Pazgier, M. / Lu, W.
History
DepositionJun 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: 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
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutrophil defensin 1
B: Neutrophil defensin 1
C: Neutrophil defensin 1
D: Neutrophil defensin 1
E: Neutrophil defensin 1
F: Neutrophil defensin 1
G: Neutrophil defensin 1
H: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0369
Polymers26,9448
Non-polymers921
Water3,765209
1
A: Neutrophil defensin 1
B: Neutrophil defensin 1
C: Neutrophil defensin 1
D: Neutrophil defensin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5645
Polymers13,4724
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-21 kcal/mol
Surface area6910 Å2
MethodPISA
2
E: Neutrophil defensin 1
F: Neutrophil defensin 1
G: Neutrophil defensin 1
H: Neutrophil defensin 1


Theoretical massNumber of molelcules
Total (without water)13,4724
Polymers13,4724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-21 kcal/mol
Surface area6560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.002, 62.575, 42.498
Angle α, β, γ (deg.)90.00, 99.69, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein/peptide
Neutrophil defensin 1 / Defensin / alpha 1 / HNP-1 / HP-1 / HP1 / HP 1-56 / Neutrophil defensin 2 / HNP-2 / HP-2 / HP2


Mass: 3367.951 Da / Num. of mol.: 8 / Mutation: I20A, L25A / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P59665
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.82 Å3/Da / Density % sol: 32.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

-
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: May 27, 2009 / Details: CONFOCAL
RadiationMonochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.66→50 Å / Num. all: 22854 / Num. obs: 22465 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.5
Reflection shellResolution: 1.66→1.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.448 / Mean I/σ(I) obs: 1.6 / % possible all: 84.1

-
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 3GNY

3gny


Resolution: 1.7→20 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.857 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23088 1085 5.1 %RANDOM
Rwork0.1851 ---
obs0.18765 20118 99.18 %-
all-20466 --
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 mean: 29.513 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å21.93 Å2
2---0.36 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1815 0 6 209 2030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0221895
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9391.9222567
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7775226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.46118.11885
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.615250
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8081531
X-RAY DIFFRACTIONr_chiral_restr0.1550.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211503
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.1611.51159
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.72721801
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9043736
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3794.5766
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 83 -
Rwork0.272 1441 -
obs--96.76 %

+
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://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