[English] 日本語
Yorodumi
- PDB-3uc7: Trp-cage cyclo-TC1 - monoclinic crystal form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3uc7
TitleTrp-cage cyclo-TC1 - monoclinic crystal form
ComponentsCyclo-TC1
KeywordsDE NOVO PROTEIN / mini-protein / Trp-cage / cyclic peptide / multimer / protein-protein interaction
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsScian, M. / Le Trong, I. / Stenkamp, R.E. / Andersen, N.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal and NMR structures of a Trp-cage mini-protein benchmark for computational fold prediction.
Authors: Scian, M. / Lin, J.C. / Le Trong, I. / Makhatadze, G.I. / Stenkamp, R.E. / Andersen, N.H.
History
DepositionOct 26, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Aug 15, 2012Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Cyclo-TC1
B: Cyclo-TC1
C: Cyclo-TC1
D: Cyclo-TC1
E: Cyclo-TC1
F: Cyclo-TC1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9368
Polymers12,8656
Non-polymers712
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-43 kcal/mol
Surface area6080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.697, 48.748, 35.259
Angle α, β, γ (deg.)90.000, 116.910, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein/peptide
Cyclo-TC1


Mass: 2144.240 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: solid-phase synthesis and cyclization
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 1.72 Å3/Da / Density % sol: 28.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 2.5
Details: 0.2 M Tris-HCl, 0.2 M magnesium chloride, 2.0 M sodium chloride, pH 2.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.82 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 3, 2009
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82 Å / Relative weight: 1
ReflectionResolution: 0.99→50 Å / Num. all: 39329 / Num. obs: 39329 / % possible obs: 81.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.4 % / Rmerge(I) obs: 0.089 / Χ2: 1.13 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
0.99-1.033.714980.928131.1
1.03-1.07521491.007144.60.783
1.07-1.116.131551.022165.60.714
1.11-1.177.639881.033182.60.519
1.17-1.259.445471.077194.30.489
1.25-1.3412.147141.145197.90.387
1.34-1.4814.747421.179198.40.295
1.48-1.6915.247981.069199.10.159
1.69-2.1315.248321.166199.60.09
2.13-5013.349061.23199.60.068

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2LL5

2ll5


Resolution: 1.1→35.39 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.2024 / WRfactor Rwork: 0.1564 / Occupancy max: 1 / Occupancy min: 0.1 / FOM work R set: 0.7959 / SU B: 1.834 / SU ML: 0.038 / SU R Cruickshank DPI: 0.0368 / SU Rfree: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.037 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1937 1695 5.1 %RANDOM
Rwork0.1491 ---
obs0.1514 33543 94.81 %-
all-33543 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 47.19 Å2 / Biso mean: 18.274 Å2 / Biso min: 8.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.91 Å20 Å20.13 Å2
2---0.58 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.1→35.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 2 107 1015
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.021973
X-RAY DIFFRACTIONr_bond_other_d0.0030.02701
X-RAY DIFFRACTIONr_angle_refined_deg2.4021.9851335
X-RAY DIFFRACTIONr_angle_other_deg1.18631687
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7755128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg22.40822.63238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6961596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.126158
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0231141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02189
X-RAY DIFFRACTIONr_mcbond_it4.6524660
X-RAY DIFFRACTIONr_mcbond_other3.1834272
X-RAY DIFFRACTIONr_mcangle_it6.0961032
X-RAY DIFFRACTIONr_scbond_it6.736313
X-RAY DIFFRACTIONr_scangle_it7.79710303
X-RAY DIFFRACTIONr_rigid_bond_restr2.10911674
X-RAY DIFFRACTIONr_sphericity_free18.6435113
X-RAY DIFFRACTIONr_sphericity_bonded9.73951637
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 88 -
Rwork0.245 1838 -
all-1926 -
obs--73.62 %

+
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://pdbjlvh1.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