[English] 日本語
Yorodumi
- PDB-5wo1: Chaperone Spy H96L bound to Im7 L18A L19A L37A (Im7 un-modeled) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wo1
TitleChaperone Spy H96L bound to Im7 L18A L19A L37A (Im7 un-modeled)
ComponentsPeriplasmic chaperone Spy
KeywordsCHAPERONE
Function / homology
Function and homology information


chaperone-mediated protein folding / protein folding chaperone / response to organic cyclic compound / unfolded protein binding / outer membrane-bounded periplasmic space / protein homodimerization activity
Similarity search - Function
: / LTXXQ motif family protein / LTXXQ motif family protein / Four Helix Bundle (Hemerythrin (Met), subunit A) - #1490 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
GLUTAMIC ACID / IMIDAZOLE / Periplasmic chaperone Spy
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsHorowitz, S. / Koldewey, P. / Martin, R. / Bardwell, J.C.A.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2016
Title: Visualizing chaperone-assisted protein folding.
Authors: Horowitz, S. / Salmon, L. / Koldewey, P. / Ahlstrom, L.S. / Martin, R. / Quan, S. / Afonine, P.V. / van den Bedem, H. / Wang, L. / Xu, Q. / Trievel, R.C. / Brooks, C.L. / Bardwell, J.C.
History
DepositionAug 1, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionAug 16, 2017ID: 5IOE
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Periplasmic chaperone Spy
B: Periplasmic chaperone Spy
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,36037
Polymers23,0312
Non-polymers2,33035
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.090, 43.090, 258.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-207-

ZN

21A-210-

ZN

31B-314-

HOH

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Periplasmic chaperone Spy / Spheroplast protein Y


Mass: 11515.285 Da / Num. of mol.: 2 / Fragment: UNP residues 52-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli) / References: UniProt: P77754

-
Non-polymers , 5 types, 149 molecules

#2: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 27 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GLU / GLUTAMIC ACID


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.61 Å3/Da / Density % sol: 52.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8 / Details: PEG 3000, imidazole, zinc acetate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97933 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.87→30.48 Å / Num. obs: 21505 / % possible obs: 100 % / Redundancy: 9.6 % / Net I/σ(I): 13.8

-
Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5INA

5ina
PDB Unreleased entry


Resolution: 1.87→30.469 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 1999 9.34 %
Rwork0.2068 --
obs0.2107 21405 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→30.469 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1416 0 64 114 1594
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0141582
X-RAY DIFFRACTIONf_angle_d1.2442117
X-RAY DIFFRACTIONf_dihedral_angle_d25.784645
X-RAY DIFFRACTIONf_chiral_restr0.054226
X-RAY DIFFRACTIONf_plane_restr0.006288
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.91680.36721380.31541339X-RAY DIFFRACTION100
1.9168-1.96860.34311410.2621369X-RAY DIFFRACTION100
1.9686-2.02650.28081350.24221314X-RAY DIFFRACTION100
2.0265-2.09190.28311420.22951371X-RAY DIFFRACTION100
2.0919-2.16670.24191390.20681350X-RAY DIFFRACTION100
2.1667-2.25340.21921390.19811353X-RAY DIFFRACTION100
2.2534-2.35590.26181410.18691364X-RAY DIFFRACTION100
2.3559-2.48010.23611400.19941354X-RAY DIFFRACTION100
2.4801-2.63540.21581410.19221371X-RAY DIFFRACTION100
2.6354-2.83870.27881420.20331392X-RAY DIFFRACTION100
2.8387-3.12410.22941440.21171398X-RAY DIFFRACTION100
3.1241-3.57560.23581470.20751428X-RAY DIFFRACTION100
3.5756-4.50260.22911480.17351429X-RAY DIFFRACTION100
4.5026-30.47320.25711620.2241574X-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)
15.2875-4.31670.76486.12371.86822.40730.37890.0374-0.0516-0.0635-0.3491-0.45770.0310.1515-0.09250.359-0.13730.08030.3085-0.00460.2759-2.6555-28.859122.5907
23.94825.2634-3.14488.2195-5.86983.4062-0.09280.0379-0.4683-0.0822-0.2007-0.56510.1366-0.0360.26670.4189-0.14030.09830.2561-0.03380.2547.8185-10.015422.2437
38.44853.187-4.82619.1636-4.55263.784-0.32861.6372-0.0209-0.85080.23080.47320.7654-1.00070.0520.3603-0.08050.06860.4448-0.03520.2272.6757.12698.6259
45.2935-0.2117-0.57119.61876.78074.86040.07341.41810.2075-1.7202-0.74292.0364-0.7123-1.21110.62370.25360.0466-0.10460.6086-0.1310.8222-21.9783-26.481313.9149
50.7618-1.5409-1.11664.7438-1.24059.19670.0494-0.3748-0.69840.48790.17510.8707-0.1536-0.8686-0.16430.378-0.06430.13610.34180.08720.4322.39741.993621.2551
67.08256.4591.50198.51224.1372.3055-0.13020.22560.4535-0.0457-0.07630.8336-0.0004-0.21170.20110.2956-0.116-0.03890.28780.08130.2463-4.4351-15.498325.3736
76.1080.81670.46173.48960.28334.4302-0.39261.232-0.3863-0.7011-0.23430.58240.9181-0.2437-0.04270.314-0.37040.10390.5511-0.17760.3642-9.5897-33.123412.554
87.1378-2.35081.99986.90095.84482.0001-0.42010.7178-0.04762.7141.13930.6583.22941.7859-0.78311.69950.3359-0.57841.3820.83471.4572-5.2142-33.549932.5302
99.2035-5.7612-6.6546.07540.93769.1752-0.10661.5699-1.5722-0.3776-0.84532.24251.3847-1.74460.73350.4439-0.15720.12880.6802-0.19520.56318.36822.72351.8694
106.6897-1.34421.91896.7214-5.41924.62060.1420.2465-0.3909-0.3135-0.2860.10060.9072-0.05940.20980.3632-0.00610.07870.39760.02660.240418.9239-0.25154.8241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1( CHAIN A AND RESID 57:74 )
2X-RAY DIFFRACTION2( CHAIN A AND RESID 75:106 )
3X-RAY DIFFRACTION3( CHAIN A AND RESID 107:124 )
4X-RAY DIFFRACTION4( CHAIN B AND RESID 29:46 )
5X-RAY DIFFRACTION5( CHAIN B AND RESID 54:74 )
6X-RAY DIFFRACTION6( CHAIN B AND RESID 75:106 )
7X-RAY DIFFRACTION7( CHAIN B AND RESID 107:123 )
8X-RAY DIFFRACTION8( CHAIN A AND RESID 214:214 )
9X-RAY DIFFRACTION9( CHAIN A AND RESID 28:35 )
10X-RAY DIFFRACTION10( CHAIN A AND RESID 36:47 )

+
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