[English] 日本語
Yorodumi
- PDB-5aq7: DARPin-based Crystallization Chaperones exploit Molecular Geometr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aq7
TitleDARPin-based Crystallization Chaperones exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
ComponentsD12_DB04V3
KeywordsCHAPERONE / CRYSTALLIZATION CHAPERONE / DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) / RIGID DOMAIN FUSION
Function / homologyAnkyrin repeat-containing domain / Beta-lactamase / DD-peptidase/beta-lactamase superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta / MALONATE ION
Function and homology information
Biological speciesSYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBatyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.
CitationJournal: J.Mol.Biol. / Year: 2016
Title: Darpin-Based Crystallization Chaperones Exploit Molecular Geometry as a Screening Dimension in Protein Crystallography
Authors: Batyuk, A. / Wu, Y. / Honegger, A. / Heberling, M. / Plueckthun, A.
History
DepositionSep 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2016Group: Database references
Revision 1.2May 25, 2016Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: 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: D12_DB04V3
B: D12_DB04V3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,6154
Polymers90,4112
Non-polymers2042
Water7,963442
1
A: D12_DB04V3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4103
Polymers45,2051
Non-polymers2042
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D12_DB04V3


Theoretical massNumber of molelcules
Total (without water)45,2051
Polymers45,2051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.040, 156.240, 68.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein D12_DB04V3


Mass: 45205.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNTHETIC CONSTRUCT (others) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K-12 / Variant (production host): XL1-BLUE
#2: Chemical ChemComp-MLI / MALONATE ION


Mass: 102.046 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H2O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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: 2.25 Å3/Da / Density % sol: 45.3 % / Description: NONE
Crystal growpH: 7.5
Details: PEG3350 20.0% W/V, SODIUM MALONATE 0.2 M, BIS TRIS PROPANE 0.1M, PH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2012 / Details: RH COATED MERIDIONALLY FOCUSSING MIRROR
RadiationMonochromator: FIXED-EXIT LN2 COOLED DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→43.49 Å / Num. obs: 50274 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12 % / Biso Wilson estimate: 34.29 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.59
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 11.3 % / Mean I/σ(I) obs: 1.36 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3DTM AND 1SVX CHAIN A

3dtm

1svx


Resolution: 2.1→43.488 Å / SU ML: 0.27 / σ(F): 1.99 / Phase error: 25.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 2514 5 %
Rwork0.1899 --
obs0.1919 50258 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.488 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6150 0 14 442 6606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036306
X-RAY DIFFRACTIONf_angle_d0.7148566
X-RAY DIFFRACTIONf_dihedral_angle_d12.3762326
X-RAY DIFFRACTIONf_chiral_restr0.04997
X-RAY DIFFRACTIONf_plane_restr0.0031117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.14030.36791370.33132609X-RAY DIFFRACTION99
2.1403-2.1840.34291360.30642582X-RAY DIFFRACTION100
2.184-2.23150.31521380.2852610X-RAY DIFFRACTION100
2.2315-2.28340.31961380.26912621X-RAY DIFFRACTION100
2.2834-2.34050.33361370.25492612X-RAY DIFFRACTION100
2.3405-2.40380.29811390.25232637X-RAY DIFFRACTION100
2.4038-2.47450.3011380.23212631X-RAY DIFFRACTION100
2.4745-2.55440.26351390.22022629X-RAY DIFFRACTION100
2.5544-2.64570.26471380.2132626X-RAY DIFFRACTION100
2.6457-2.75160.23381390.20962637X-RAY DIFFRACTION100
2.7516-2.87680.27981390.21622636X-RAY DIFFRACTION100
2.8768-3.02840.26571390.2172637X-RAY DIFFRACTION100
3.0284-3.21810.27851390.20592653X-RAY DIFFRACTION100
3.2181-3.46650.24331410.1812676X-RAY DIFFRACTION100
3.4665-3.81520.18971410.16072670X-RAY DIFFRACTION100
3.8152-4.36680.1871410.13312694X-RAY DIFFRACTION100
4.3668-5.49990.16991440.14022728X-RAY DIFFRACTION100
5.4999-43.49760.171510.16872856X-RAY DIFFRACTION100
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)
11.5765-0.08730.61992.29240.65138.8356-0.0650.1229-0.1404-0.20350.01130.26690.1586-0.12210.0470.2898-0.0219-0.00640.2881-0.00650.4061-25.57245.9434-54.7317
21.46540.20061.04222.28420.11913.25440.01940.11190.02350.21460.0918-0.0481-0.24570.2342-0.09850.3690.0460.01920.2879-0.02270.2855-11.521725.6411-11.1449
31.917-0.32361.01012.94520.89321.97240.02580.2317-0.1318-0.01070.1063-0.02880.03160.3459-0.13590.32010.03710.06390.3881-0.00430.2279-11.947319.7746-21.1223
42.1827-0.3057-2.40221.33230.6155.1623-0.2434-0.0146-0.3244-0.0744-0.0882-0.12310.6536-0.10710.28260.5955-0.11530.0870.3874-0.03440.405-28.598966.7269-12.0766
51.4777-0.2737-0.94195.07672.91063.36670.02260.13590.0901-0.1106-0.30350.4382-0.1511-0.34370.21260.3987-0.0214-0.00330.3273-0.03620.3268-11.864645.3061-47.0838
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 13 THROUGH 170 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 171 THROUGH 285 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 286 THROUGH 418 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 13 THROUGH 170 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 171 THROUGH 418 )

+
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://pdbjlc1.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