[English] 日本語
Yorodumi
- PDB-4z2o: High resolution crystal structure of short hoefavidin-hoef-peptid... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4z2o
TitleHigh resolution crystal structure of short hoefavidin-hoef-peptide complex
Components
  • Avidin family
  • Hoef-peptide
Keywordsbiotin binding protein / protein binding / high affinity system / bacterial avidins / biotin
Function / homology
Function and homology information


biotin binding / protein homodimerization activity / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHoeflea phototrophica DFL-43 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.17 Å
AuthorsLivnah, O. / Avraham, O.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Hoefavidin: A dimeric bacterial avidin with a C-terminal binding tail.
Authors: Avraham, O. / Meir, A. / Fish, A. / Bayer, E.A. / Livnah, O.
History
DepositionMar 30, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Dec 6, 2017Group: Database references / Category: pdbx_database_related
Item: _pdbx_database_related.db_id / _pdbx_database_related.db_name
Revision 1.4Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Avidin family
P: Hoef-peptide


Theoretical massNumber of molelcules
Total (without water)15,5772
Polymers15,5772
Non-polymers00
Water2,324129
1
A: Avidin family
P: Hoef-peptide

A: Avidin family
P: Hoef-peptide


Theoretical massNumber of molelcules
Total (without water)31,1544
Polymers31,1544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z1
Buried area5540 Å2
ΔGint-31 kcal/mol
Surface area11750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.940, 37.940, 155.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-238-

HOH

21A-308-

HOH

-
Components

#1: Protein Avidin family


Mass: 14341.508 Da / Num. of mol.: 1 / Fragment: unp residues 21-154
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hoeflea phototrophica DFL-43 (bacteria)
Gene: HPDFL43_17171 / Production host: Escherichia coli (E. coli) / References: UniProt: A9D857
#2: Protein/peptide Hoef-peptide


Mass: 1235.339 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hoeflea phototrophica DFL-43 (bacteria)
Production host: Escherichia coli (E. coli) / References: UniProt: A9D857*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NaCl, 0.1 M Bis-Tris pH 6.2-7.0 and 1.1-1.5 M ammonium sulfate
PH range: 6.2-7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.96 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.17→50 Å / Num. obs: 39465 / % possible obs: 99 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 13.5
Reflection shellResolution: 1.17→1.21 Å / Rmerge(I) obs: 0.602

-
Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z27
Resolution: 1.17→38.96 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 1.156 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16576 1972 5 %RANDOM
Rwork0.13885 ---
obs0.14018 37382 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.377 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å2-0 Å2
2--0.04 Å2-0 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 1.17→38.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1035 0 0 129 1164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021087
X-RAY DIFFRACTIONr_bond_other_d0.0010.02945
X-RAY DIFFRACTIONr_angle_refined_deg1.3441.9151491
X-RAY DIFFRACTIONr_angle_other_deg0.72632185
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.73626.2548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80215152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0870.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211303
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
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_it1.2051.159561
X-RAY DIFFRACTIONr_mcbond_other1.1921.155560
X-RAY DIFFRACTIONr_mcangle_it1.6551.738701
X-RAY DIFFRACTIONr_mcangle_other1.6591.743702
X-RAY DIFFRACTIONr_scbond_it1.8211.398526
X-RAY DIFFRACTIONr_scbond_other1.7611.382524
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3091.994787
X-RAY DIFFRACTIONr_long_range_B_refined3.46311.1041274
X-RAY DIFFRACTIONr_long_range_B_other3.22410.5821239
X-RAY DIFFRACTIONr_rigid_bond_restr1.74432031
X-RAY DIFFRACTIONr_sphericity_free28.256554
X-RAY DIFFRACTIONr_sphericity_bonded8.29752075
LS refinement shellResolution: 1.17→1.2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 152 -
Rwork0.24 2518 -
obs--93.1 %

+
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