[English] 日本語
Yorodumi
- PDB-1bb1: CRYSTAL STRUCTURE OF A DESIGNED, THERMOSTABLE HETEROTRIMERIC COIL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1bb1
TitleCRYSTAL STRUCTURE OF A DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
Components(DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL) x 3
KeywordsDE NOVO PROTEIN DESIGN / COILED COIL
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.8 Å
AuthorsNautiyal, S. / Alber, T.
Citation
Journal: Protein Sci. / Year: 1999
Title: Crystal structure of a designed, thermostable, heterotrimeric coiled coil.
Authors: Nautiyal, S. / Alber, T.
#1: Journal: Biochemistry / Year: 1995
Title: A Designed Heterotrimeric Coiled Coil
Authors: Nautiyal, S. / Woolfson, D.N. / King, D.S. / Alber, T.
History
DepositionApr 28, 1998Processing site: BNL
Revision 1.0Feb 2, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
B: DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
C: DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2474
Polymers11,2113
Non-polymers351
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-47 kcal/mol
Surface area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)21.930, 35.010, 66.460
Angle α, β, γ (deg.)90.00, 93.70, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein/peptide DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL


Mass: 3703.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#2: Protein/peptide DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL


Mass: 3839.451 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#3: Protein/peptide DESIGNED, THERMOSTABLE HETEROTRIMERIC COILED COIL


Mass: 3668.370 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others)
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mMTris-HCl1reservoir
350 mM1reservoirMgCl2
425 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.8 Å / Num. obs: 9067 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.036 / Net I/σ(I): 14.2
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.097 / Mean I/σ(I) obs: 8 / Rsym value: 0.083 / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 99.2 %

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
CCP4(SCALA)data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→6 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED INDIVIDUAL B'S / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 1004 10.9 %RANDOM
Rwork0.208 ---
obs0.208 9134 99.2 %-
Displacement parametersBiso mean: 18.8 Å2
Refinement stepCycle: LAST / Resolution: 1.8→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms774 0 1 125 900
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
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_deg0.636
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d16.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.5
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.71.5
X-RAY DIFFRACTIONx_mcangle_it2.362
X-RAY DIFFRACTIONx_scbond_it3.582
X-RAY DIFFRACTIONx_scangle_it5.9492.5
LS refinement shellResolution: 1.8→1.88 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.384 121 10.6 %
Rwork0.307 984 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PROTEIN_REP.PARAM
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg16.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.5
LS refinement shell
*PLUS
Rfactor obs: 0.307

+
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