1PB0 | pdb_00001pb0

YCDX PROTEIN IN AUTOINHIBITED STATE

PDB DOI: https://doi.org/10.2210/pdb1PB0/pdb

Classification: STRUCTURAL GENOMICS, UNKNOWN FUNCTION
Organism(s): Escherichia coli
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-05-14 Released: 2004-05-25
Deposition Author(s): Teplyakov, A., Obmolova, G., Khil, P.P., Camerini-Otero, R.D., Gilliland, G.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Work:
0.164 (Depositor), 0.170 (DCC)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Autoregulation of YcdX protein

Teplyakov, A., Obmolova, G., Khil, P.P., Camerini-Otero, R.D., Gilliland, G.L.

To be published.

Macromolecule Content

Total Structure Weight: 82.03 kDa
Atom Count: 6,181
Modeled Residue Count: 706
Deposited Residue Count: 735
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hypothetical protein ycdX	A, B, C	245	Escherichia coli	Mutation(s): 0 Gene Names: YCDX EC: 3.1.3
UniProt
Find proteins for P75914 (Escherichia coli (strain K12)) Explore P75914 Go to UniProtKB: P75914
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P75914
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain M [auth B] SDF format, chain T [auth C] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain M [auth B] MOL2 format, chain T [auth C] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain M [auth B] mmCIF format, chain T [auth C] mmCIF format, chain H [auth A]	G [auth A], H [auth A], M [auth B], T [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain M [auth B] Focus chain T [auth C]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain L [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], Q [auth C], R [auth C], S [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain S [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain O [auth B] SDF format, chain U [auth C] SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain N [auth B] MOL2 format, chain I [auth A] MOL2 format, chain O [auth B] MOL2 format, chain U [auth C] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain N [auth B] mmCIF format, chain I [auth A] mmCIF format, chain O [auth B] mmCIF format, chain U [auth C] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain N [auth B]	I [auth A] N [auth B] O [auth B] P [auth B] U [auth C] I [auth A], N [auth B], O [auth B], P [auth B], U [auth C], V [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C] Interactions & Density Focus chain I [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain U [auth C] Focus chain V [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Work: 0.164 (Depositor), 0.170 (DCC)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.13	α = 90
b = 77.33	β = 103.17
c = 82.28	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2004-05-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2004-05-25
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2023-08-16
Changes: Data collection, Database references, Derived calculations, Refinement description