[English] 日本語
Yorodumi
- PDB-3rdq: Crystal structure of R7-2 streptavidin complexed with desthiobiotin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rdq
TitleCrystal structure of R7-2 streptavidin complexed with desthiobiotin
ComponentsStreptavidin
KeywordsBIOTIN BINDING PROTEIN / Streptavidin variants / improved desthiobiotin binding / opened loop destabilization
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-DTB / NICKEL (II) ION / Streptavidin
Similarity search - Component
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsMalashkevich, V.N. / Magalhaes, M. / Czecster, C.M. / Guan, R. / Levy, M. / Almo, S.C.
CitationJournal: Protein Sci. / Year: 2011
Title: Evolved streptavidin mutants reveal key role of loop residue in high-affinity binding.
Authors: Magalhaes, M.L. / Czekster, C.M. / Guan, R. / Malashkevich, V.N. / Almo, S.C. / Levy, M.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 6, 2016Group: Non-polymer description
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Sep 13, 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Streptavidin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4476
Polymers15,9661
Non-polymers4805
Water2,504139
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.275, 57.275, 183.742
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-192-

HOH

21A-237-

HOH

31A-264-

HOH

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Streptavidin /


Mass: 15966.381 Da / Num. of mol.: 1 / Fragment: UNP Residues 37-164 / Mutation: T90S, W108V, L110T, F29L, S52G, R53S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avidinii (bacteria) / Plasmid: pCR2.1-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: P22629

-
Non-polymers , 5 types, 144 molecules

#2: Chemical ChemComp-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N2O3
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 139 / 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: 2.36 Å3/Da / Density % sol: 47.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.1 M Na-acetate, pH 5.0, 2 M Na-formate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 10, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20681 / % possible obs: 99.5 % / Redundancy: 9.4 % / Rmerge(I) obs: 0.052 / Χ2: 1.592 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.667.80.54219811.41197.5
1.66-1.729.40.45720301.0181100
1.72-1.89.70.30520341.2351100
1.8-1.99.70.20720491.31100
1.9-2.029.80.14920361.5481100
2.02-2.179.80.10320611.8461100
2.17-2.399.80.07820911.841100
2.39-2.749.80.05720731.7971100
2.74-3.459.60.04321152.243199.8
3.45-508.80.02322111.579197.7

-
Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.86 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.5 Å
Translation2.5 Å40.5 Å

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.2phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RDO

3rdo


Resolution: 1.6→19.98 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1878 / WRfactor Rwork: 0.1637 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8947 / SU B: 2.435 / SU ML: 0.043 / SU R Cruickshank DPI: 0.0745 / SU Rfree: 0.0752 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1903 1061 5.1 %RANDOM
Rwork0.1614 ---
obs0.1628 20645 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 65.7 Å2 / Biso mean: 24.775 Å2 / Biso min: 12.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms918 0 29 139 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211002
X-RAY DIFFRACTIONr_angle_refined_deg1.5211.921377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3775137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.15324.540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.67215136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.974153
X-RAY DIFFRACTIONr_chiral_restr0.1140.2159
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02760
X-RAY DIFFRACTIONr_mcbond_it1.1093.5628
X-RAY DIFFRACTIONr_mcangle_it2.773501005
X-RAY DIFFRACTIONr_scbond_it4.83650374
X-RAY DIFFRACTIONr_scangle_it1.4124.5365
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 84 -
Rwork0.25 1351 -
all-1435 -
obs--96.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.09540.10350.01990.7146-0.13450.4728-0.0071-0.00170.0694-0.03150.05080.08750.0205-0.1154-0.0437-0.046-0.0101-0.0021-0.01560.0042-0.023914.041524.6301-2.3677
21.0469-0.4617-0.37371.4015-1.04993.7727-0.07320.16920.22450.08680.0464-0.10810.0491-0.1280.02680.0124-0.0227-0.0174-0.0231-0.0281-0.010322.069324.5487-7.7618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 134
2X-RAY DIFFRACTION2A300 - 304

+
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