[English] 日本語
Yorodumi
- PDB-3q9u: In silico and in vitro co-evolution of a high affinity complement... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q9u
TitleIn silico and in vitro co-evolution of a high affinity complementary protein-protein interface
Components
  • CoA binding protein
  • consensus ankyrin repeat
KeywordsPROTEIN BINDING / DE NOVO PROTEIN / Structural Genomics / Israel Structural Proteomics Center / ISPC / Prb-binding designed ankyrin repeat
Function / homologyAnkyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / COENZYME A
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKaranicolas, J. / Corn, J.E. / Chen, I. / Joachimiak, L.A. / Dym, O. / Chung, S. / Albeck, S. / Unger, T. / Hu, W. / Liu, G. ...Karanicolas, J. / Corn, J.E. / Chen, I. / Joachimiak, L.A. / Dym, O. / Chung, S. / Albeck, S. / Unger, T. / Hu, W. / Liu, G. / Delbecq, S. / Montelione, G.T. / Spiegel, C. / Liu, D. / Baker, D. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Mol.Cell / Year: 2011
Title: A de novo protein binding pair by computational design and directed evolution.
Authors: Karanicolas, J. / Corn, J.E. / Chen, I. / Joachimiak, L.A. / Dym, O. / Peck, S.H. / Albeck, S. / Unger, T. / Hu, W. / Liu, G. / Delbecq, S. / Montelione, G.T. / Spiegel, C.P. / Liu, D.R. / Baker, D.
History
DepositionJan 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Database references
Revision 1.3Sep 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CoA binding protein
B: CoA binding protein
C: consensus ankyrin repeat
D: consensus ankyrin repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7076
Polymers65,1724
Non-polymers1,5352
Water0
1
A: CoA binding protein
C: consensus ankyrin repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3543
Polymers32,5862
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CoA binding protein
D: consensus ankyrin repeat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3543
Polymers32,5862
Non-polymers7681
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.901, 57.620, 58.230
Angle α, β, γ (deg.)89.96, 90.14, 113.44
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein CoA binding protein


Mass: 16097.753 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Protein consensus ankyrin repeat


Mass: 16488.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#3: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H36N7O16P3S

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.69 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M NaF 20 % PEG 3350, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 292K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 28, 2009
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27228 / % possible obs: 83.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

-
Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.5_2) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3q9n

3q9n


Resolution: 2.3→37.738 Å / SU ML: 0.49 / σ(F): 2 / Phase error: 34.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3175 1263 5.13 %Random
Rwork0.24 ---
obs0.2441 24632 86.2 %-
all-28575 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.416 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.3331 Å2-0.4377 Å20.6283 Å2
2--1.0332 Å20.3077 Å2
3----0.7001 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4521 0 96 0 4617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094697
X-RAY DIFFRACTIONf_angle_d1.3276397
X-RAY DIFFRACTIONf_dihedral_angle_d21.1921764
X-RAY DIFFRACTIONf_chiral_restr0.085732
X-RAY DIFFRACTIONf_plane_restr0.01822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.39220.36461410.26312433X-RAY DIFFRACTION80
2.3922-2.50110.36131270.25092724X-RAY DIFFRACTION90
2.5011-2.63290.33111460.25392796X-RAY DIFFRACTION92
2.6329-2.79780.36571610.2572749X-RAY DIFFRACTION92
2.7978-3.01370.38531430.27042738X-RAY DIFFRACTION90
3.0137-3.31690.38631590.27082583X-RAY DIFFRACTION87
3.3169-3.79640.28881270.25412433X-RAY DIFFRACTION80
3.7964-4.78160.27531240.19422435X-RAY DIFFRACTION81
4.7816-37.74310.22281350.19692478X-RAY DIFFRACTION83
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)
11.4431-0.2190.05461.2653-0.33481.1925-0.0629-0.08970.0204-0.08520.00850.05480.00310.022600.0535-0.01090.00340.0951-0.00090.0966-2.61757.459-17.9631
20.6686-0.64140.48442.6491-0.47421.28390.12680.06920.1627-0.3035-0.2756-0.14820.10240.0821-0.00060.08750.01910.04790.0840.0210.069636.1137-7.07489.1888
31.5211-0.6291-0.70480.9130.70711.43160.08610.1960.26280.09290.1048-0.1549-0.0193-0.2856-0.00020.08170.01890.00330.13920.05060.187720.862810.5514-24.8081
40.7721-0.01480.24090.9938-0.34921.2940.2003-0.01860.0135-0.096-0.16410.1340.0503-0.19880.00010.2122-0.0234-0.01720.1412-0.03250.124817.4882-22.045115.4056
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