[English] 日本語
Yorodumi
- PDB-5izs: De novo design of protein homo-oligomers with modular hydrogen bo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5izs
TitleDe novo design of protein homo-oligomers with modular hydrogen bond network-mediated specificity
ComponentsDesigned protein 5L6HC3_1
KeywordsDE NOVO PROTEIN / rosetta / de novo design
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsSankaran, B. / Zwart, P.H. / Pereira, J.H. / Baker, D. / Boyken, S. / Chen, Z. / Oberdorfer, G.
CitationJournal: Science / Year: 2016
Title: De novo design of protein homo-oligomers with modular hydrogen-bond network-mediated specificity.
Authors: Boyken, S.E. / Chen, Z. / Groves, B. / Langan, R.A. / Oberdorfer, G. / Ford, A. / Gilmore, J.M. / Xu, C. / DiMaio, F. / Pereira, J.H. / Sankaran, B. / Seelig, G. / Zwart, P.H. / Baker, D.
History
DepositionMar 25, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 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: Designed protein 5L6HC3_1
B: Designed protein 5L6HC3_1
C: Designed protein 5L6HC3_1
D: Designed protein 5L6HC3_1
E: Designed protein 5L6HC3_1
F: Designed protein 5L6HC3_1


Theoretical massNumber of molelcules
Total (without water)67,8706
Polymers67,8706
Non-polymers00
Water2,252125
1
A: Designed protein 5L6HC3_1
B: Designed protein 5L6HC3_1
C: Designed protein 5L6HC3_1


Theoretical massNumber of molelcules
Total (without water)33,9353
Polymers33,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-46 kcal/mol
Surface area13180 Å2
MethodPISA
2
D: Designed protein 5L6HC3_1
E: Designed protein 5L6HC3_1
F: Designed protein 5L6HC3_1


Theoretical massNumber of molelcules
Total (without water)33,9353
Polymers33,9353
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-53 kcal/mol
Surface area13340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.670, 72.670, 88.240
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11C-118-

HOH

DetailsTrimer according to SEC-MALS and SAXS data

-
Components

#1: Protein
Designed protein 5L6HC3_1


Mass: 11311.688 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 1.98 Å3/Da / Density % sol: 37.94 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium Fluoride, 0.1 M MES pH 5.5 , 20 % PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.36→51.24 Å / Num. obs: 21259 / % possible obs: 99 % / Redundancy: 6.4 % / Biso Wilson estimate: 22.6 Å2 / CC1/2: 0.9 / Rmerge(I) obs: 0.148 / Net I/σ(I): 12
Reflection shellHighest resolution: 2.36 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.715 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→51.237 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2688 1091 5.13 %
Rwork0.2453 --
obs0.2465 21249 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→51.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3971 0 0 125 4096
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044005
X-RAY DIFFRACTIONf_angle_d0.6285345
X-RAY DIFFRACTIONf_dihedral_angle_d15.7731682
X-RAY DIFFRACTIONf_chiral_restr0.021629
X-RAY DIFFRACTIONf_plane_restr0.002702
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3602-2.46760.31141350.26832554X-RAY DIFFRACTION100
2.4676-2.59770.30321400.25172531X-RAY DIFFRACTION100
2.5977-2.76050.30431430.25052483X-RAY DIFFRACTION99
2.7605-2.97360.29991350.2632541X-RAY DIFFRACTION99
2.9736-3.27280.30021190.24492566X-RAY DIFFRACTION100
3.2728-3.74620.23791540.22282479X-RAY DIFFRACTION99
3.7462-4.71930.20421270.21242543X-RAY DIFFRACTION99
4.7193-51.24950.30511380.29122461X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0779-0.02650.0318-0.0341-0.01430.0065-0.05670.02510.0590.07330.39060.29760.0379-0.1317-00.17460.10950.07980.17070.05610.15754.077821.6969-52.0694
20.01590.1556-0.00410.08450.04020.00440.0463-0.07920.1102-0.0434-0.078-0.0773-0.3037-0.0065-00.06260.078-0.01890.2349-0.04680.08974.0332.2614-51.4135
30.1172-0.019-0.04860.2154-0.03830.00810.056-0.0747-0.01640.01190.129-0.06650.1337-0.067300.09570.0292-0.05170.182-0.02550.164814.580915.6068-51.2362
40.0805-0.1985-0.0331-0.17060.03720.00990.0318-0.1596-0.1813-0.3383-0.00650.10360.3182-0.31810-0.023-0.0662-0.04730.25920.07840.21425.320110.3143-50.6115
50.05730.21-0.00640.02670.01130.00940.06710.00560.10070.11190.1076-0.1256-0.31460.014400.10240.0889-0.02660.1865-0.03450.13913.894628.0793-48.1624
6-0.1124-0.07550.0864-0.1214-0.05280.01980.304-0.1707-0.22680.2046-0.1985-0.21250.30620.2514-0-0.00160.08240.01630.1613-0.05810.171522.906523.0978-49.5644
7-0.1866-0.010.0548-0.2556-0.03210.01660.03720.07570.15410.6650.6928-0.70710.09580.2646-0-0.2541-0.180.20570.19190.02160.0519-6.463319.8146-11.4239
80.0315-0.10980.0219-0.0227-0.05330.0247-0.24360.11920.0913-0.017-0.3209-0.3241-0.30470.1123-00.054-0.1095-0.0480.1917-0.00240.0809-5.714830.1765-11.7574
90.00130.0105-0.0130.03940.00830.001-0.10450.15790.15860.40130.1607-0.1287-0.0716-0.07190-0.2313-0.13760.17240.30950.08340.0828-16.150926.673-12.6387
100.02140.20680.05610.1548-0.070.02270.2503-0.2698-0.2511-0.19340.3184-0.0162-0.23-0.321800.1846-0.01620.01610.26720.03160.1415-25.692322.2063-8.7518
110.06120.0808-0.0780.0349-0.01040.01440.11480.0696-0.0730.02720.01480.11970.0835-0.03700.1732-0.0152-0.03440.1782-0.00410.1408-17.775714.7855-12.9218
120.00850.13790.02190.02240.05590.0160.1989-0.1714-0.29890.0240.0984-0.15440.26780.1806-00.13490.0680.03840.0008-0.13510.1041-8.76549.0073-7.737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 82 )
3X-RAY DIFFRACTION3chain 'B' and (resid 6 through 44 )
4X-RAY DIFFRACTION4chain 'B' and (resid 45 through 82 )
5X-RAY DIFFRACTION5chain 'C' and (resid 4 through 41 )
6X-RAY DIFFRACTION6chain 'C' and (resid 42 through 85 )
7X-RAY DIFFRACTION7chain 'D' and (resid 3 through 44 )
8X-RAY DIFFRACTION8chain 'D' and (resid 45 through 84 )
9X-RAY DIFFRACTION9chain 'E' and (resid 4 through 41 )
10X-RAY DIFFRACTION10chain 'E' and (resid 42 through 84 )
11X-RAY DIFFRACTION11chain 'F' and (resid 3 through 41 )
12X-RAY DIFFRACTION12chain 'F' and (resid 42 through 82 )

+
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