[English] 日本語
Yorodumi
- PDB-4yxz: Computationally designed left-handed alpha/alpha toroid with 9 repeats -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yxz
TitleComputationally designed left-handed alpha/alpha toroid with 9 repeats
ComponentsdTor_9x31L
KeywordsDE NOVO PROTEIN / Rosetta / toroid / alpha helix / computationally designed / left-handed
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.496 Å
AuthorsDoyle, L. / Stoddard, B.L. / Bradley, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM49857 United States
CitationJournal: Nature / Year: 2015
Title: Rational design of alpha-helical tandem repeat proteins with closed architectures.
Authors: Doyle, L. / Hallinan, J. / Bolduc, J. / Parmeggiani, F. / Baker, D. / Stoddard, B.L. / Bradley, P.
History
DepositionMar 23, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2015Group: Database references
Revision 1.2Jan 6, 2016Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dTor_9x31L


Theoretical massNumber of molelcules
Total (without water)30,8261
Polymers30,8261
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.736, 72.019, 86.186
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein dTor_9x31L


Mass: 30825.730 Da / Num. of mol.: 1 / Fragment: dTor_9x31L / Source method: obtained synthetically / Details: Rosetta designed / Source: (synth.) synthetic construct (others)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 0.1 M Sodium citrate, 1.0 M Ammonium phosphate monobasic

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.496→50 Å / Num. obs: 9450 / % possible obs: 99.2 % / Redundancy: 10 % / Biso Wilson estimate: 36.35 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.023 / Rrim(I) all: 0.079 / Χ2: 1.267 / Net I/av σ(I): 30.42 / Net I/σ(I): 14.5 / Num. measured all: 94932
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.496-2.544.50.2584140.960.1330.2921.04791.2
2.54-2.5950.2424490.9730.1180.270.99994.9
2.59-2.645.60.2564480.9750.1160.2821.04898.9
2.64-2.696.50.2134760.9840.0880.2311.055100
2.69-2.758.30.1694560.9910.0620.181.151100
2.75-2.8210.40.1844700.9930.0590.1931.206100
2.82-2.8910.70.1464670.9950.0460.1531.328100
2.89-2.9610.60.134660.9950.0420.1371.359100
2.96-3.0510.80.1194660.9960.0380.1251.36100
3.05-3.1510.90.1164710.9960.0370.1221.399100
3.15-3.26110.1154690.9960.0360.1211.294100
3.26-3.3911.20.0884690.9980.0270.0921.341100
3.39-3.5511.40.0794800.9980.0240.0831.444100
3.55-3.7311.70.0754760.9990.0220.0781.419100
3.73-3.9711.80.0714690.9980.0210.0751.43100
3.97-4.2711.90.0614860.9990.0180.0641.411100
4.27-4.7120.064840.9990.0180.0621.397100
4.7-5.3812.10.0574950.9990.0170.061.08699.6
5.38-6.7811.90.064950.9990.0180.0630.915100
6.78-5010.80.0525440.9980.0160.0551.11598.4

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASER2.5.6phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computationally designed molecule

Resolution: 2.496→29.98 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3279 936 10.01 %
Rwork0.2248 8419 -
obs0.2346 9355 98.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.69 Å2 / Biso mean: 34.7397 Å2 / Biso min: 15.52 Å2
Refinement stepCycle: final / Resolution: 2.496→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2011 0 0 0 2011
Num. residues----278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082037
X-RAY DIFFRACTIONf_angle_d1.0382779
X-RAY DIFFRACTIONf_chiral_restr0.035350
X-RAY DIFFRACTIONf_plane_restr0.004339
X-RAY DIFFRACTIONf_dihedral_angle_d14.834683
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.496-2.62750.3751250.24451122124794
2.6275-2.7920.39061330.27231189132299
2.792-3.00740.35661330.25031177131098
3.0074-3.30970.39011300.27241192132299
3.3097-3.78780.30221360.216612251361100
3.7878-4.76910.30051350.19321217135299
4.7691-29.98220.29351440.2071297144199

+
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