[English] 日本語
Yorodumi
- PDB-1rav: RECOMBINANT AVIDIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rav
TitleRECOMBINANT AVIDIN
ComponentsAVIDIN
KeywordsGLYCOPROTEIN / AVIDIN / BIOTIN BINDING PROTEIN / CALYCINS / UP-AND-DOWN BETA BARREL
Function / homology
Function and homology information


biotin binding / antibacterial humoral response / extracellular region
Similarity search - Function
Avidin-like / Avidin-like, conserved site / Avidin-like domain signature. / Avidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRosano, C. / Arosio, P. / Bolognesi, M.
Citation
Journal: Eur.J.Biochem. / Year: 1998
Title: Biochemical characterization and crystal structure of a recombinant hen avidin and its acidic mutant expressed in Escherichia coli.
Authors: Nardone, E. / Rosano, C. / Santambrogio, P. / Curnis, F. / Corti, A. / Magni, F. / Siccardi, A.G. / Paganelli, G. / Losso, R. / Apreda, B. / Bolognesi, M. / Sidoli, A. / Arosio, P.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: Crystal Structure of Apo-Avidin from Hen Egg-White
Authors: Pugliese, L. / Malcovati, M. / Coda, A. / Bolognesi, M.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Three-Dimensional Structures of Avidin and the Avidin-Biotin Complex
Authors: Livnah, O. / Bayer, E.A. / Wilchek, M. / Sussman, J.L.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: Three-Dimensional Structure of the Tetragonal Crystal Form of Egg-White Avidin in its Functional Complex with Biotin at 2.7 A Resolution
Authors: Pugliese, L. / Coda, A. / Malcovati, M. / Bolognesi, M.
History
DepositionMar 27, 1998Processing site: BNL
Revision 1.0Jul 15, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AVIDIN
B: AVIDIN


Theoretical massNumber of molelcules
Total (without water)28,5822
Polymers28,5822
Non-polymers00
Water1,44180
1
A: AVIDIN
B: AVIDIN

A: AVIDIN
B: AVIDIN


Theoretical massNumber of molelcules
Total (without water)57,1644
Polymers57,1644
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area10210 Å2
ΔGint-49 kcal/mol
Surface area21920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.690, 80.790, 43.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein AVIDIN /


Mass: 14291.058 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Cell: EGG / Cell line: BL21 / Cellular location: CYTOPLASM (WHITE) / Plasmid: BL21 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P02701
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.42 Å3/Da / Density % sol: 58.7 %
Crystal growMethod: vapor diffusion / pH: 7.2
Details: RECOMBINANT AVIDIN WAS CRYSTALLIZED FROM 9% W/V PEG 8000. PH 7.2 0.05 M TRIS BUFFER AT 22 C BY VAPOUR DIFFUSION TECHNIQUES., vapor diffusion
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
29 %mass/vPEG80001drop
30.05 MTris-HCl1droppH7.2
42.0 Mammonium sulfate1reservoir
50.05 Msodium phosphate1reservoirpH5.7

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→20.5 Å / Num. obs: 13827 / % possible obs: 95 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15
Reflection shellResolution: 2.2→2.7 Å / % possible all: 93.1
Reflection
*PLUS
Num. measured all: 48932

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
CCP4data reduction
AMoREphasing
TNT5Erefinement
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVE

1ave


Resolution: 2.2→20.2 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflection
all0.17 13480 -
obs-13480 95 %
Solvent computationSolvent model: TNT / Bsol: 150 Å2 / ksol: 0.77 e/Å3
Refinement stepCycle: LAST / Resolution: 2.2→20.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 0 80 2032
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01619944.5
X-RAY DIFFRACTIONt_angle_deg2.61126967.5
X-RAY DIFFRACTIONt_dihedral_angle_d20.53811940
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.017485.5
X-RAY DIFFRACTIONt_gen_planes0.01828821.9
X-RAY DIFFRACTIONt_it3.466199417
X-RAY DIFFRACTIONt_nbd0.0624112
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg20.5380
X-RAY DIFFRACTIONt_planar_d0.0175.5
X-RAY DIFFRACTIONt_plane_restr0.01821.9

+
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