[English] 日本語
Yorodumi
- PDB-4hb1: A DESIGNED FOUR HELIX BUNDLE PROTEIN. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hb1
TitleA DESIGNED FOUR HELIX BUNDLE PROTEIN.
ComponentsDHP1
KeywordsDESIGNED HELICAL BUNDLE
Function / homologyImmunoglobulin FC, subunit C / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsSchafmeister, C.E. / Laporte, S.L. / Miercke, L.J.W. / Stroud, R.M.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: A designed four helix bundle protein with native-like structure.
Authors: Schafmeister, C.E. / LaPorte, S.L. / Miercke, L.J. / Stroud, R.M.
History
DepositionNov 10, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DHP1


Theoretical massNumber of molelcules
Total (without water)11,8153
Polymers11,8151
Non-polymers02
Water362
1
A: DHP1

A: DHP1


Theoretical massNumber of molelcules
Total (without water)23,6316
Polymers23,6312
Non-polymers04
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/31
Unit cell
Length a, b, c (Å)51.900, 51.900, 61.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
DetailsTHE MOLECULE CONTAINS A CRYSTALLOGRAPHIC TW0-FOLD AXIS OF SYMMETRY THROUGH THE CENTER OF THE 4-HELIX BUNDLE. THIS UNUSUAL ARRANGEMENT IS DUE TO THE SYNTHETIC NATURE OF THE MOLECULE IN WHICH THE SAME SEQUENCE SEGMENTS REPEAT. THE SYMMETRY OPERATION REQUIRED TO GENERATE THE ENTIRE BUNDLE IS (-Y+1, -X+1, 1/3-Z) AND IS GIVEN IN REMARK 350 AS AN OPERATOR ON THE COORDINATES IN THIS ENTRY.

-
Components

#1: Protein DHP1


Mass: 11815.356 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DE NOVO DESIGN A 108 AMINO ACID PROTEIN WAS DESIGNED AND CONSTRUCTED FROM A REDUCED ALPHABET OF SEVEN AMINO ACIDS. THE 2.9 ANGSTROM CRYSTAL STRUCTURE CONFIRMS THAT THE PROTEIN IS A FOUR ...Details: DE NOVO DESIGN A 108 AMINO ACID PROTEIN WAS DESIGNED AND CONSTRUCTED FROM A REDUCED ALPHABET OF SEVEN AMINO ACIDS. THE 2.9 ANGSTROM CRYSTAL STRUCTURE CONFIRMS THAT THE PROTEIN IS A FOUR HELIX BUNDLE, AS IT WAS DESIGNED TO BE. THE COMPLETE 108 RESIDUE SEQUENCE IS PRESENTED ON SEQRES RECORDS BELOW. THE HELICES WERE CONNECTED BY LOOPS OF 3, 4, 3 GLYCINES, RESPECTIVELY. THE MOLECULE CONTAINS A CRYSTALLOGRAPHIC TW0-FOLD AXIS OF SYMMETRY THROUGH THE CENTER OF THE 4-HELIX BUNDLE. THIS UNUSUAL ARRANGEMENT IS DUE TO THE SYNTHETIC NATURE OF THE MOLECULE IN WHICH THE SAME SEQUENCE SEGMENTS REPEAT. THE SYMMETRY OPERATION REQUIRED TO GENERATE THE ENTIRE BUNDLE IS (-Y+1, -X+1, 1/3-Z) AND IS GIVEN IN REMARK 350 AS AN OPERATOR ON THE COORDINATES IN THIS ENTRY.
Source: (gene. exp.) synthetic construct (others) / Description: DE NOVO DESIGNED FOUR HELIX BUNDLE PROTEIN / Gene: SYNTHETIC GENE DHP1 / Plasmid: PMAL-C2 / Gene (production host): SYNTHETIC GENE DHP1 / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-BLUE
#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Compound detailsA 108 AMINO ACID PROTEIN WAS DESIGNED AND CONSTRUCTED FROM A REDUCED ALPHABET OF SEVEN AMINO ACIDS. ...A 108 AMINO ACID PROTEIN WAS DESIGNED AND CONSTRUCTED FROM A REDUCED ALPHABET OF SEVEN AMINO ACIDS. THE 2.9 ANGSTROM CRYSTAL STRUCTURE CONFIRMS THAT THE PROTEIN IS A FOUR HELIX BUNDLE, AS IT WAS DESIGNED TO BE. THE COMPLETE 108 RESIDUE SEQUENCE IS PRESENTED ON SEQRES RECORDS BELOW. THE HELICES WERE CONNECTED BY LOOPS OF 3, 4, 3 GLYCINES, RESPECTIVELY.

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growpH: 8.6
Details: 65% AMMONIUM SULPHATE, 3% ISOPROPANOL, 100MM TRIS, PH 8.6
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
165 %satammonium salfate1reservoir
23 %isopropanol1reservoir
3100 mMTris1reservoir
432.5 %satammonium sulfate1drop
550 mMTris1drop
64 mg/mlDHP11drop

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Type: SSRL / Wavelength: 1.5418
DetectorDate: May 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.9 Å / Num. obs: 19263 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 8.2 % / Biso Wilson estimate: 60 Å2 / Rsym value: 0.055
Reflection shellHighest resolution: 2.9 Å
Reflection
*PLUS
Num. obs: 1212 / Num. measured all: 19263 / Rmerge(I) obs: 0.055

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MODEL HELIX

Resolution: 2.9→7.5 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.284 110 10 %RANDOM
Rwork0.234 ---
obs0.234 1102 96 %-
Refinement stepCycle: LAST / Resolution: 2.9→7.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms592 0 4 2 598
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
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_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.7
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

+
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