[English] 日本語
Yorodumi
- PDB-7cpz: Crystal structure of Streptoavidin-C1 from Streptomyces cinamonensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7cpz
TitleCrystal structure of Streptoavidin-C1 from Streptomyces cinamonensis
ComponentsMature Streptoavidin-C1
KeywordsANTIMICROBIAL PROTEIN / Avidin / Antifungal / Biotin
Function / homologyAvidin / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / biotin binding / extracellular region / BIOTIN / Avidin
Function and homology information
Biological speciesStreptomyces sp. H036 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsJeon, B.J. / Kim, S. / Lee, J.-H. / Kim, M.S. / Hwang, K.Y.
CitationJournal: Iucrj / Year: 2021
Title: Insights into the structure of mature streptavidin C1 from Streptomyces cinnamonensis reveal the self-binding of the extension C-terminal peptide to biotin-binding sites.
Authors: Jeon, B.J. / Kim, S. / Kim, M.S. / Lee, J.H. / Kim, B.S. / Hwang, K.Y.
History
DepositionAug 8, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 21, 2021Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: Mature Streptoavidin-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4172
Polymers20,1721
Non-polymers2441
Water88349
1
A: Mature Streptoavidin-C1
hetero molecules

A: Mature Streptoavidin-C1
hetero molecules

A: Mature Streptoavidin-C1
hetero molecules

A: Mature Streptoavidin-C1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,6668
Polymers80,6894
Non-polymers9774
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,-y-1,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area9540 Å2
ΔGint-49 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.997, 57.997, 74.847
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z

-
Components

#1: Protein Mature Streptoavidin-C1 / Streptoavidin-C1


Mass: 20172.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. H036 (bacteria) / Gene: ADK98_07690 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0M8UVL7
#2: Chemical ChemComp-BTN / BIOTIN


Mass: 244.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 1.56 Å3/Da / Density % sol: 21.16 %
Crystal growTemperature: 298 K / Method: batch mode / Details: PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→41 Å / Num. obs: 4763 / % possible obs: 99.8 % / Redundancy: 20 % / Rpim(I) all: 0.09 / Rrim(I) all: 0.335 / Net I/σ(I): 7.51
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 229 / Rpim(I) all: 0.258 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BC3

2bc3


Resolution: 2.5→37.42 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2611 221 -
Rwork0.206 --
obs0.2085 4763 99.8 %
Displacement parametersBiso mean: 32.38 Å2
Refinement stepCycle: LAST / Resolution: 2.5→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 16 49 986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052964
X-RAY DIFFRACTIONf_angle_d0.85621314
X-RAY DIFFRACTIONf_chiral_restr0.0559139
X-RAY DIFFRACTIONf_plane_restr0.0034167
X-RAY DIFFRACTIONf_dihedral_angle_d22.7386332

+
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