[English] 日本語
Yorodumi
- PDB-5v2o: De Novo Design of Novel Covalent Constrained Meso-size Peptide Sc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v2o
TitleDe Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique Tertiary Structures
ComponentsTP2
KeywordsDE NOVO PROTEIN / De Novo Design / Covalent core / constrained mess-size peptide
Function / homology1,3,5-BENZENETRICARBOXYLIC ACID
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.2 Å
AuthorsDang, B. / Wu, H. / Mulligan, V.K. / Mravic, M. / Wu, Y. / Lemmin, T. / Ford, A. / Silva, D. / Baker, D. / DeGrado, W.F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures.
Authors: Dang, B. / Wu, H. / Mulligan, V.K. / Mravic, M. / Wu, Y. / Lemmin, T. / Ford, A. / Silva, D.A. / Baker, D. / DeGrado, W.F.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TP2
B: TP2
C: TP2
D: TP2
E: TP2
F: TP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,00826
Polymers37,1406
Non-polymers3,86820
Water6,431357
1
A: TP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9114
Polymers6,1901
Non-polymers7213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,9114
Polymers6,1901
Non-polymers7213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0035
Polymers6,1901
Non-polymers8134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,0035
Polymers6,1901
Non-polymers8134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: TP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5884
Polymers6,1901
Non-polymers3983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: TP2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,5924
Polymers6,1901
Non-polymers4023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.770, 55.340, 58.040
Angle α, β, γ (deg.)89.79, 108.15, 109.52
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
TP2


Mass: 6190.015 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: De novo designed molecule / Source: (synth.) synthetic construct (others)

-
Non-polymers , 5 types, 377 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical
ChemComp-TMM / 1,3,5-BENZENETRICARBOXYLIC ACID


Mass: 210.140 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M MES, pH 6.5, 2.0 M ((NH4)2SO4 , 5 %w/v PEG 400,Protein: 10mg/mL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.82648 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82648 Å / Relative weight: 1
ReflectionResolution: 1.2→54.81 Å / Num. obs: 127440 / % possible obs: 92.4 % / Redundancy: 3 % / CC1/2: 0.99 / Net I/σ(I): 7.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSversion 0.58data reduction
XSCALEVersion 10/15/2015data scaling
Arcimboldophasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.2→54.8 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.363 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.035 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17848 6236 5.1 %RANDOM
Rwork0.14401 ---
obs0.14583 114886 95.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.247 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20.21 Å20.19 Å2
2---0.18 Å20.4 Å2
3----0.19 Å2
Refinement stepCycle: 1 / Resolution: 1.2→54.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2574 0 201 357 3132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0192902
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9012.0483871
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85386
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.80426.61118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9315495
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2851520
X-RAY DIFFRACTIONr_chiral_restr0.2020.2456
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.022078
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it7.3711.5841496
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it9.2082.3991889
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.0932.0371406
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.47124.3714547
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr8.84232902
X-RAY DIFFRACTIONr_sphericity_free30.4515224
X-RAY DIFFRACTIONr_sphericity_bonded21.11853028
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.277 429 -
Rwork0.271 8429 -
obs--93.6 %

+
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