[English] 日本語
Yorodumi
- PDB-1df8: S45A MUTANT OF STREPTAVIDIN IN COMPLEX WITH BIOTIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1df8
TitleS45A MUTANT OF STREPTAVIDIN IN COMPLEX WITH BIOTIN
ComponentsPROTEIN (STREPTAVIDIN)
KeywordsBINDING PROTEIN / BIOTIN BINDING PROTEIN / BIOTIN
Function / homology
Function and homology information


biotin binding / 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
BIOTIN / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsHyre, D.E. / Le Trong, I. / Freitag, S. / Stenkamp, R.E. / Stayton, P.S.
CitationJournal: Protein Sci. / Year: 2000
Title: Ser45 plays an important role in managing both the equilibrium and transition state energetics of the streptavidin-biotin system.
Authors: Hyre, D.E. / Le Trong, I. / Freitag, S. / Stenkamp, R.E. / Stayton, P.S.
History
DepositionNov 18, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 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 1.4Aug 9, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0194
Polymers26,5312
Non-polymers4892
Water5,765320
1
A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules

A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0398
Polymers53,0614
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area11590 Å2
ΔGint-38 kcal/mol
Surface area17780 Å2
MethodPISA
2
A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules

A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules

A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules

A: PROTEIN (STREPTAVIDIN)
B: PROTEIN (STREPTAVIDIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,07716
Polymers106,1238
Non-polymers1,9548
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
MethodPQS
Unit cell
Length a, b, c (Å)46.200, 93.900, 104.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-479-

HOH

21B-372-

HOH

-
Components

#1: Protein PROTEIN (STREPTAVIDIN) / CORE STREPTAVIDIN


Mass: 13265.336 Da / Num. of mol.: 2 / Fragment: CORE, RESIDUES 13-139 / Mutation: S45A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 1 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 294 K / pH: 4.5
Details: 40% SATURATED AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, pH 4.5, temperature 294.K
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 %satammonium sulfate11
20.1 Msodium acetate11
33.8 mMbiotin11

-
Data collection

DiffractionMean temperature: 127 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 23, 1998
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→10 Å / Num. all: 167399 / Num. obs: 30427 / % possible obs: 82.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 2.15
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 1 % / Rmerge(I) obs: 0.103 / % possible all: 4
Reflection
*PLUS
Num. measured all: 167399

-
Processing

Software
NameClassification
X-PLORmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SWA

1swa


Resolution: 1.51→10 Å / Num. parameters: 872 / Num. restraintsaints: 795 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3029 10 %RANDOM
Rwork0.169 ---
all0.166 30289 --
obs0.162 30289 84.5 %-
Refine analyzeOccupancy sum hydrogen: 1695 / Occupancy sum non hydrogen: 2129
Refinement stepCycle: LAST / Resolution: 1.51→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 32 320 2130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.031
X-RAY DIFFRACTIONs_zero_chiral_vol0.04
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.05
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.06
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Num. reflection all: 30298 / σ(F): 4 / % reflection Rfree: 10 % / Rfactor all: 0.169 / Rfactor obs: 0.165 / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.029
X-RAY DIFFRACTIONs_planar_d0.031
X-RAY DIFFRACTIONs_plane_restr0.04

+
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://pdbjlvh1.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