1S5U | pdb_00001s5u

Crystal Structure of Hypothetical Protein EC709 from Escherichia coli

PDB DOI: https://doi.org/10.2210/pdb1S5U/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-01-21 Released: 2004-05-11
Deposition Author(s): Kim, Y., Joachimiak, A., Skarina, T., Savchenko, A., Edwards, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free:
0.230 (Depositor), 0.229 (DCC)
R-Value Work:
0.200 (Depositor), 0.200 (DCC)
R-Value Observed:
0.200 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Crystal Structure of Hypothetical Protein EC709 from Escherichia coli

Kim, Y., Joachimiak, A., Skarina, T., Savchenko, A., Edwards, A.

To be published.

Macromolecule Content

Total Structure Weight: 128.83 kDa
Atom Count: 9,316
Modeled Residue Count: 1,042
Deposited Residue Count: 1,104
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein ybgC	A, B, C, D, E A, B, C, D, E, F, G, H	138	Escherichia coli	Mutation(s): 0 Gene Names: YBGC, B0736, C0815, Z0904, ECS0771, SF0561, S0574 EC: 3.1.2
UniProt
Find proteins for P0A8Z3 (Escherichia coli (strain K12)) Explore P0A8Z3 Go to UniProtKB: P0A8Z3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P0A8Z3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain P [auth D] SDF format, chain Q [auth E] SDF format, chain S [auth F] SDF format, chain W [auth H] SDF format, chain X [auth H] SDF format, chain V [auth G] SDF format, chain T [auth F] MOL2 format, chain I [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth F] MOL2 format, chain W [auth H] MOL2 format, chain X [auth H] MOL2 format, chain V [auth G] MOL2 format, chain T [auth F] mmCIF format, chain I [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth F] mmCIF format, chain W [auth H] mmCIF format, chain X [auth H] mmCIF format, chain V [auth G] mmCIF format, chain T [auth F]	I [auth A] K [auth B] L [auth B] M [auth C] N [auth C] I [auth A], K [auth B], L [auth B], M [auth C], N [auth C], P [auth D], Q [auth E], S [auth F], T [auth F], V [auth G], W [auth H], X [auth H]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H] Interactions & Density Focus chain I [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain S [auth F] Focus chain T [auth F] Focus chain V [auth G] Focus chain W [auth H] Focus chain X [auth H]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain R [auth E] SDF format, chain U [auth F] SDF format, chain Y [auth H] SDF format, chain O [auth C] MOL2 format, chain J [auth A] MOL2 format, chain R [auth E] MOL2 format, chain U [auth F] MOL2 format, chain Y [auth H] MOL2 format, chain O [auth C] mmCIF format, chain J [auth A] mmCIF format, chain R [auth E] mmCIF format, chain U [auth F] mmCIF format, chain Y [auth H] mmCIF format, chain O [auth C]	J [auth A], O [auth C], R [auth E], U [auth F], Y [auth H]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain O [auth C] Focus chain R [auth E] Focus chain U [auth F] Focus chain Y [auth H] Interactions & Density Focus chain J [auth A] Focus chain O [auth C] Focus chain R [auth E] Focus chain U [auth F] Focus chain Y [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.230 (Depositor), 0.229 (DCC)
R-Value Work: 0.200 (Depositor), 0.200 (DCC)
R-Value Observed: 0.200 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.108	α = 103.47
b = 70.187	β = 95.15
c = 71.525	γ = 97.58

Software Package:

Software Name	Purpose
CNS	refinement
SBC-Collect	data collection
HKL-2000	data scaling
autoSHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2004-05-11

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2004-05-11
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: 2024-02-14
Changes: Data collection, Database references, Derived calculations