[English] 日本語
Yorodumi
- PDB-2qcb: T7-tagged full-length streptavidin complexed with ruthenium ligand -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2qcb
TitleT7-tagged full-length streptavidin complexed with ruthenium ligand
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / streptavidin / t7-tag / artificial transfer hydrogenase
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
Chem-KYS / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsLe Trong, I. / Creus, M. / Pordea, A. / Ward, T.R. / Stenkamp, R.E.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2008
Title: X-ray structure and designed evolution of an artificial transfer hydrogenase
Authors: Creus, M. / Pordea, A. / Rossel, T. / Sardo, A. / Letondor, C. / Ivanova, A. / Letrong, I. / Stenkamp, R.E. / Ward, T.R.
History
DepositionJun 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 600HETEROGEN The ligand KYS has considerable molecular motion and disorder. The Ruthenium metal is not ...HETEROGEN The ligand KYS has considerable molecular motion and disorder. The Ruthenium metal is not modeled in confomer B. The SO2N group attached to the linker has rotational disorder and has been modeled as conformer C.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,2662
Polymers16,6121
Non-polymers6541
Water2,018112
1
A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules

A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,0658
Polymers66,4484
Non-polymers2,6174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z1
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_555y,x,-z1
Buried area13440 Å2
ΔGint-99 kcal/mol
Surface area17990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.651, 57.651, 183.823
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-403-

HOH

21A-445-

HOH

31A-511-

HOH

DetailsThe biological assembly is a tetramer generated by the deposited chain and three additional subunits generated by application of these crystallographic symmetry operations: 1-x,1-y,z; y,x,-z; 1-y,1-x,-z.

-
Components

#1: Protein Streptavidin /


Mass: 16612.119 Da / Num. of mol.: 1 / Mutation: S112K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: Pet11B / Production host: Escherichia coli (E. coli) / References: UniProt: P22629
#2: Chemical ChemComp-KYS / N-(4-{[(2-AMINOETHYL)AMINO]SULFONYL}PHENYL)-5-[(3AS,4S,6AR)-2-OXOHEXAHYDRO-1H-THIENO[3,4-D]IMIDAZOL-4-YL]PENTANAMIDE-(1,2,3,4,5,6-ETA)-BENZENE-CHLORO-RUTHENIUM(III)


Mass: 654.187 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H31ClN5O4RuS2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: protein, 26 mg/ml in water. 4-5x molar excess of ligand. reservoir, 1.0 M sodium citrate, 0.1 M cacodylate buffer, pH 6.5 , VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 15, 2006 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. all: 21478 / Num. obs: 21478 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Redundancy: 10.7 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.034 / Χ2: 1.069 / Net I/σ(I): 63.4
Reflection shellResolution: 1.53→1.58 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.6 / Num. unique all: 650 / Χ2: 1.069 / % possible all: 27.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→19.9 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.651 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 970 5.1 %RANDOM
Rwork0.168 ---
all0.169 19020 --
obs0.169 19020 99.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.954 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms916 0 37 112 1065
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0211009
X-RAY DIFFRACTIONr_bond_other_d0.0010.02616
X-RAY DIFFRACTIONr_angle_refined_deg1.5741.9851417
X-RAY DIFFRACTIONr_angle_other_deg2.00931495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3725121
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.91823.8142
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.4915134
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.947155
X-RAY DIFFRACTIONr_chiral_restr0.0860.2150
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021129
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02216
X-RAY DIFFRACTIONr_nbd_refined0.2060.2163
X-RAY DIFFRACTIONr_nbd_other0.2090.2607
X-RAY DIFFRACTIONr_nbtor_refined0.190.2475
X-RAY DIFFRACTIONr_nbtor_other0.0910.2502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.262
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2270.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.219
X-RAY DIFFRACTIONr_mcbond_it1.2421.5758
X-RAY DIFFRACTIONr_mcbond_other0.3191.5258
X-RAY DIFFRACTIONr_mcangle_it1.4972944
X-RAY DIFFRACTIONr_scbond_it2.0893529
X-RAY DIFFRACTIONr_scangle_it2.4924.5440
X-RAY DIFFRACTIONr_rigid_bond_restr2.37632150
X-RAY DIFFRACTIONr_sphericity_free4.7723112
X-RAY DIFFRACTIONr_sphericity_bonded2.04331593
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 64 -
Rwork0.247 1173 -
obs-1237 90.62 %

+
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