[English] 日本語
Yorodumi
- PDB-3tes: Crystal Structure of Tencon -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3tes
TitleCrystal Structure of Tencon
ComponentsTencon
KeywordsDE NOVO PROTEIN / Fibronectin type III domain / FN3 / consensus design
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLuo, J. / Jacobs, S. / Teplyakov, A. / Obmolova, G. / O'Neil, K. / Gilliland, G.
CitationJournal: Protein Eng.Des.Sel. / Year: 2012
Title: Design of novel FN3 domains with high stability by a consensus sequence approach.
Authors: Jacobs, S.A. / Diem, M.D. / Luo, J. / Teplyakov, A. / Obmolova, G. / Malia, T. / Gilliland, G.L. / O'Neil, K.T.
History
DepositionAug 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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: Tencon
B: Tencon
C: Tencon
D: Tencon


Theoretical massNumber of molelcules
Total (without water)42,9954
Polymers42,9954
Non-polymers00
Water2,144119
1
A: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tencon


Theoretical massNumber of molelcules
Total (without water)10,7491
Polymers10,7491
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.720, 87.580, 56.220
Angle α, β, γ (deg.)90.00, 103.92, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Tencon


Mass: 10748.873 Da / Num. of mol.: 4 / Source method: obtained synthetically
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 297 K / Method: vapor diffusion / pH: 3.5
Details: 0.1 M sodium citrate, 6% PEG 4000, pH 3.5, VAPOR DIFFUSION, temperature 297K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD
RadiationMonochromator: VariMax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15396 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.078

-
Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERphasing
PHENIX(phenix.refine: 1.7_650)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→26.56 Å / SU ML: 0.34 / σ(F): 1.39 / Phase error: 36.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2972 384 2.51 %Random
Rwork0.2419 ---
obs0.2432 15313 96.15 %-
all-15313 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.482 Å2 / ksol: 0.386 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.3614 Å2-0 Å2-14.0994 Å2
2---7.2761 Å20 Å2
3---10.6375 Å2
Refinement stepCycle: LAST / Resolution: 2.5→26.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2828 0 0 119 2947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032903
X-RAY DIFFRACTIONf_angle_d0.7883951
X-RAY DIFFRACTIONf_dihedral_angle_d12.0231051
X-RAY DIFFRACTIONf_chiral_restr0.063447
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5002-2.86160.35721270.31084998X-RAY DIFFRACTION97
2.8616-3.60390.29061310.24155000X-RAY DIFFRACTION97
3.6039-26.56150.27891260.22054931X-RAY DIFFRACTION94
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)
10.04180.03950.06240.4926-0.01810.1225-0.1224-0.11050.0079-0.02550.17260.2116-0.04950.0082-0.03990.12510.01360.02750.16110.01290.1369-4.538929.58716.4562
20.1581-0.10060.17610.4791-0.04710.217-0.0855-0.06040.09690.16480.0906-0.1547-0.10460.0124-0.01690.11910.00420.0290.1609-0.02320.169113.279429.831816.3807
30.42990.0802-0.04960.192-0.00510.32520.1588-0.0582-0.13790.0705-0.10910.0157-0.0246-0.069-0.02390.1154-0.0122-0.00890.10280.00460.09493.383753.685412.4296
40.5350.12810.11680.2813-0.08530.36190.1891-0.0351-0.18390.1357-0.017-0.04750.08790.0538-0.07760.1812-0.0079-0.03780.1337-0.00950.187822.374453.583219.545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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