[English] 日本語
Yorodumi
- PDB-1vwa: STREPTAVIDIN-FSHPQNT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1vwa
TitleSTREPTAVIDIN-FSHPQNT
Components
  • PEPTIDE LIGAND CONTAINING HPQ
  • STREPTAVIDIN
KeywordsCOMPLEX (BIOTIN-BINDING PROTEIN/PEPTIDE) / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) / LINEAR PEPTIDE DISCOVERED BY PHAGE DISPLAY / COMPLEX (BIOTIN-BINDING PROTEIN-PEPTIDE) complex
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
Biological speciesStreptomyces avidinii (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsKatz, B.A. / Cass, R.T.
Citation
Journal: J.Biol.Chem. / Year: 1997
Title: In crystals of complexes of streptavidin with peptide ligands containing the HPQ sequence the pKa of the peptide histidine is less than 3.0.
Authors: Katz, B.A. / Cass, R.T.
#1: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Structure-Based Design Tools: Structural and Thermodynamic Comparison with Biotin of a Small Molecule that Binds Streptavidin with Micromolar Affinity
Authors: Katz, B.A. / Liu, B. / Cass, R.T.
#2: Journal: J.Am.Chem.Soc. / Year: 1996
Title: Preparation of a Protein-Dimerizing Ligand by Topochemistry and Structure-Based Design
Authors: Katz, B.A.
#3: Journal: J.Biol.Chem. / Year: 1995
Title: Topochemical Catalysis Achieved by Structure-Based Ligand Design
Authors: Katz, B.A. / Cass, R.T. / Liu, B. / Arze, R. / Collins, N.
#4: Journal: Chem.Biol. / Year: 1995
Title: Topochemistry for Preparing Ligands that Dimerize Receptors
Authors: Katz, B.A. / Stroud, R.M. / Collins, N. / Liu, B. / Arze, R.
#5: Journal: Biochemistry / Year: 1995
Title: Binding to Protein Targets of Peptidic Leads Discovered by Phage Display: Crystal Structures of Streptavidin-Bound Linear and Cyclic Peptide Ligands Containing the Hpq Sequence
Authors: Katz, B.A.
#6: Journal: J.Am.Chem.Soc. / Year: 1995
Title: Structure-Based Design of High Affinity Streptavidin Binding Cyclic Peptide Ligands Containing Thioether Cross-Links
Authors: Katz, B.A. / Johnson, C.R. / Cass, R.T.
History
DepositionMar 3, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Feb 14, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ


Theoretical massNumber of molelcules
Total (without water)27,5924
Polymers27,5924
Non-polymers00
Water3,225179
1
B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ

B: STREPTAVIDIN
D: STREPTAVIDIN
M: PEPTIDE LIGAND CONTAINING HPQ
P: PEPTIDE LIGAND CONTAINING HPQ


Theoretical massNumber of molelcules
Total (without water)55,1848
Polymers55,1848
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)97.030, 107.470, 48.550
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
11B-1118-

HOH

21D-1095-

HOH

31D-1095-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999757, -0.021401, -0.005364), (-0.019246, 0.727065, 0.686299), (-0.010788, 0.686235, -0.7273)
Vector: 53.1306, 0.6257, 0.2082)

-
Components

#1: Protein STREPTAVIDIN /


Mass: 12965.025 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Streptomyces avidinii (bacteria) / References: UniProt: P22629
#2: Protein/peptide PEPTIDE LIGAND CONTAINING HPQ


Mass: 830.864 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.29 Å3/Da / Density % sol: 22 %
Crystal growpH: 4
Details: SYNTHETIC MOTHER LIQUOR = 50 % SATURATED AMMONIUM SULFATE, 50 % 0.1 M POTASSIUM ACETATE., pH 4.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Pahler, A., (1987) J. Biol. Chem., 262, 13933.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130-32 %satammonium salfate1reservoir
20.1 Mpotassium acetate1reservoirpH4.0
315 mg/mlprotein1drop
415-16 %satammonium salfate1drop
50.05 Mpotassium acetate1drop

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 25792 / Redundancy: 3.8 % / Rmerge(I) obs: 0.083
Reflection
*PLUS
Highest resolution: 1.63 Å / Num. measured all: 98073

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
SAINTdata scaling
X-PLORphasing
RefinementResolution: 1.85→7.5 Å / σ(F): 2
Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 47, B 48, B 49, B 50, TERMINUS OF ARG B 53, B 67, B 68, TERMINUS OF ARG B 84, TERMINUS OF ARG B 103, ...Details: THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 47, B 48, B 49, B 50, TERMINUS OF ARG B 53, B 67, B 68, TERMINUS OF ARG B 84, TERMINUS OF ARG B 103, TERMINUS OF GLU B 116, B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, D 51, (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), PEPTIDE RESIDUES M 2, M 7. M 1 WAS NOT LOCATED OR INCLUDED IN THE MODEL. DISCRETELY DISORDERED SIDE CHAINS WHOSE OCCUPANCIES AND STRUCTURES WERE SIMULTANEOUSLY REFINED WERE B 22, D 73, D 107, AND P 1. B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A TWO-FOLD RELATED B 22. PROPER REFINEMENT WITH X-PLOR IS NOT POSSIBLE BECAUSE OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY-RELATED COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR DENSITY DUE TO THIS CONFORMER OF TYR B 22: HOH 585, HOH 1056. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THESE WATERS AND THE REST OF THE STRUCTURE. HOH 1118 IS CLOSE TO ITS SYMMETRY-RELATED EQUIVALENT AND IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THIS WATER AND THE REST OF THE STRUCTURE. BULK SOLVENT WAS REFINED. HOH 1095 OCCUPIES A PORTION OF SPACE THE SAME AS CONFORMER 2 OF B 22. HOH 595 IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1122. THE FOLLOWING ATOMS HAD WEAK DENSITY AND OCCUPANCIES WERE REFINED: B 13, B 14, B 15, B 47, B 48, B 49, B 50, TERMINUS OF ARG B 53, B 67, B 68, TERMINUS OF ARG B 84, TERMINUS OF ARG B 103, TERMINUS OF GLU B 116, B 135, D 13, D 14, D 15, D 46, D 47, D 48, D 49, D 50, D 51, (TERMINUS OF ARG D 84), (TERMINUS OF ARG D 103), PEPTIDE RESIDUES M 2, M 7. M 1 WAS NOT LOCATED OR INCLUDED IN THE MODEL. B 22 IS DISORDERED BETWEEN 2 CONFORMATIONS ONE OF WHICH OCCUPIES A SIMILAR REGION OF SPACE AS A TWO-FOLD RELATED B 22. PROPER REFINEMENT WITH X-PLOR IS NOT POSSIBLE BECAUSE OF THE OVERLAP OF ONE CONFORMER WITH THE SYMMETRY-RELATED COUNTERPART. THE FOLLOWING WATERS WERE USED TO ACCOUNT FOR DENSITY DUE TO THIS CONFORMER OF TYR B 22: HOH 585, HOH 1056. IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THESE WATERS AND THE REST OF THE STRUCTURE. HOH 1118 IS CLOSE TO ITS SYMMETRY-RELATED EQUIVALENT AND IN REFINEMENT THERE WERE NO ENERGY INTERACTIONS BETWEEN THIS WATER AND THE REST OF THE STRUCTURE. BULK SOLVENT WAS REFINED. HOH 1095 OCCUPIES A PORTION OF SPACE THE SAME AS CONFORMER 2 OF B 22. HOH 595 IS CLOSE TO A SYMMETRY-RELATED EQUIVALENT OF HOH 1122.
RfactorNum. reflection% reflection
Rfree0.259 -10 %
Rwork0.192 --
obs0.192 15514 71.4 %
Refinement stepCycle: LAST / Resolution: 1.85→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 0 179 2313
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.5
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.85→1.93 Å / % reflection obs: 42 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1FSHPQNT_PARAM19XB2_KBCO.PFSHPQNT_TOPH19XB2_KBCO.PRO
X-RAY DIFFRACTION2PARAM11_UCSF.WATTOPH19.PEP
X-RAY DIFFRACTION3PARAM19XB2_KBCO.PROTOPH19XB2_KBCO.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.5

+
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