[English] 日本語
Yorodumi
- PDB-5hrz: Computationally Designed Trimer 1na0C3_3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hrz
TitleComputationally Designed Trimer 1na0C3_3
ComponentsTPR domain protein 1na0C3_3
KeywordsDE NOVO PROTEIN / Protein Design / Designed Oligomeric Interface
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsCascio, D. / McNamara, D.E. / Fallas, J.A. / Baker, D. / Yeates, T.O.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1332907 United States
CitationJournal: Nat Chem / Year: 2017
Title: Computational design of self-assembling cyclic protein homo-oligomers.
Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D.
History
DepositionJan 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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: TPR domain protein 1na0C3_3


Theoretical massNumber of molelcules
Total (without water)14,7051
Polymers14,7051
Non-polymers00
Water25214
1
A: TPR domain protein 1na0C3_3

A: TPR domain protein 1na0C3_3

A: TPR domain protein 1na0C3_3


Theoretical massNumber of molelcules
Total (without water)44,1163
Polymers44,1163
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area3030 Å2
ΔGint-30 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.570, 83.570, 141.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
DetailsTrimer based on SEC-MALS and SAXS

-
Components

#1: Protein TPR domain protein 1na0C3_3


Mass: 14705.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21 NESG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.24 Å3/Da / Density % sol: 62.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 2.4 M sodium malonate pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.15→64.48 Å / Num. obs: 10656 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 45.92 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 20.88
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.15-2.229.20.6753.3197.8
2.2-2.260.5664.711100
2.26-2.330.4475.69199.9
2.33-2.40.3856.541100
2.4-2.480.3287.781100
2.48-2.570.21910.421100
2.57-2.660.1911.981100
2.66-2.770.1614.731100
2.77-2.90.11519.211100
2.9-3.040.09422.511100
3.04-3.20.07426.61199.8
3.2-3.40.05931.471100
3.4-3.630.05138.571100
3.63-3.920.04642.79199.8
3.92-4.290.04145.13199.8
4.29-4.80.03844.43199.5
4.8-5.540.04145.14199.7
5.54-6.790.04145.21100
6.79-9.60.03447.211100

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
BUSTER-TNTrefinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Computational model based on 1NA0

1na0


Resolution: 2.15→64.48 Å / Cor.coef. Fo:Fc: 0.9562 / Cor.coef. Fo:Fc free: 0.951 / SU R Cruickshank DPI: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.146 / SU Rfree Blow DPI: 0.132 / SU Rfree Cruickshank DPI: 0.135
RfactorNum. reflection% reflectionSelection details
Rfree0.206 946 8.89 %RANDOM
Rwork0.18 9694 --
obs0.1821 10640 99.92 %-
Displacement parametersBiso max: 115.81 Å2 / Biso mean: 48.28 Å2 / Biso min: 30.39 Å2
Baniso -1Baniso -2Baniso -3
1-3.185 Å20 Å20 Å2
2--3.185 Å20 Å2
3----6.3699 Å2
Refine analyzeLuzzati coordinate error obs: 0.256 Å
Refinement stepCycle: final / Resolution: 2.15→64.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms971 0 0 14 985
Biso mean---55.85 -
Num. residues----122
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d347SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes39HARMONIC2
X-RAY DIFFRACTIONt_gen_planes138HARMONIC5
X-RAY DIFFRACTIONt_it991HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion121SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1100SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d991HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1342HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.58
X-RAY DIFFRACTIONt_other_torsion19.27
LS refinement shellResolution: 2.15→2.4 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2048 279 9.38 %
Rwork0.1954 2696 -
all0.1963 2975 -
obs--99.92 %
Refinement TLS params.Method: refined / Origin x: -3.4942 Å / Origin y: 26.6282 Å / Origin z: -11.8166 Å
111213212223313233
T-0.0256 Å2-0.021 Å20.0217 Å2--0.096 Å20.0263 Å2---0.0561 Å2
L0.6016 °20.366 °20.0488 °2-4.9959 °20.5258 °2--1.3914 °2
S-0.0082 Å °-0.0351 Å °-0.0088 Å °0.2147 Å °-0.0137 Å °0.093 Å °0.1884 Å °-0.0794 Å °0.022 Å °
Refinement TLS groupSelection details: { A|* }

+
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