6BIE

MISREADING CHAPERONE-SUBSTRATE COMPLEXES FROM RANDOM NOISE

PDB DOI: https://doi.org/10.2210/pdb6BIE/pdb

Classification: CHAPERONE
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-01 Released: 2018-10-17
Deposition Author(s): WANG, J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.248
R-Value Work: 0.175
R-Value Observed: 0.179

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5IOG

Literature

Misreading chaperone-substrate complexes from random noise.

Wang, J.

(2018) Nat Struct Mol Biol 25: 989-990

PubMed: 30297779 Search on PubMed
DOI: https://doi.org/10.1038/s41594-018-0144-3
Primary Citation of Related Structures:
6BIE

Organizational Affiliation

Department of Molecular Biochemistry and Biophysics, Yale University, New Haven, CT, USA. jimin.wang@yale.edu.

Macromolecule Content

Total Structure Weight: 24.41 kDa
Atom Count: 1,943
Modelled Residue Count: 194
Deposited Residue Count: 194
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Periplasmic chaperone Spy	A, B	97	Escherichia coli K-12	Mutation(s): 0 Gene Names: spy, b1743, JW1732
UniProt
Find proteins for P77754 (Escherichia coli (strain K12)) Explore P77754 Go to UniProtKB: P77754
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P77754
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IMD Query on IMD Download Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain Q [auth A]	Q [auth A], R [auth A], S [auth A]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain T [auth B] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain K [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain T [auth B] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain K [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain T [auth B] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain K [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], T [auth B], U [auth B], V [auth B], W [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain T [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth A] SDF format, chain Z [auth B] SDF format, chain L [auth A] SDF format, chain O [auth A] SDF format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain L [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain L [auth A] mmCIF format, chain O [auth A] mmCIF format, chain Y [auth B]	L [auth A] M [auth A] N [auth A] O [auth A] P [auth A] L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Y [auth B], Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Y [auth B] Focus chain Z [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain X [auth B] MOL2 format, chain X [auth B] mmCIF format, chain X [auth B]	X [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain X [auth B] Interactions & Density Focus chain X [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.77 Å
R-Value Free: 0.248
R-Value Work: 0.175
R-Value Observed: 0.179
Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.96	α = 90
b = 42.96	β = 90
c = 258.169	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-10-17

Deposition Author(s):

WANG, J.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01 GM022778

Revision History (Full details and data files)

Version 1.0: 2018-10-17
Type: Initial release
Version 1.1: 2018-10-24
Changes: Data collection, Database references
Version 1.2: 2018-11-14
Changes: Data collection, Database references
Version 1.3: 2019-02-20
Changes: Author supporting evidence, Data collection
Version 1.4: 2020-01-01
Changes: Author supporting evidence
Version 1.5: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description