6NRU | pdb_00006nru

Crystal Structure of the Alpha-ribazole Phosphatase from Shigella flexneri

PDB DOI: https://doi.org/10.2210/pdb6NRU/pdb

Classification: HYDROLASE
Organism(s): Shigella flexneri 2a
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2019-01-24 Released: 2019-03-06
Deposition Author(s): Kim, Y., Gu, M., Shatsman, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.218 (Depositor), 0.217 (DCC)
R-Value Work:
0.179 (Depositor), 0.180 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the Alpha-ribazole Phosphatase from Shigella flexneri

Kim, Y., Gu, M., Shatsman, S., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 292.2 kDa
Atom Count: 20,711
Modeled Residue Count: 2,425
Deposited Residue Count: 2,472
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CobC	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	206	Shigella flexneri 2a	Mutation(s): 0 Gene Names: cobC_1, SAMEA3891773_00492 EC: 3.1.3.73

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain O [auth A] MOL2 format, chain X [auth C] MOL2 format, chain O [auth A] mmCIF format, chain X [auth C] mmCIF format, chain O [auth A]	O [auth A], X [auth C]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain X [auth C] Interactions & Density Focus chain O [auth A] Focus chain X [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain RA [auth H] SDF format, chain P [auth A] SDF format, chain NA [auth G] SDF format, chain KB [auth L] SDF format, chain JB [auth L] SDF format, chain IB [auth L] SDF format, chain IA [auth F] SDF format, chain DA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain RA [auth H] MOL2 format, chain P [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain KB [auth L] MOL2 format, chain JB [auth L] MOL2 format, chain IB [auth L] MOL2 format, chain IA [auth F] MOL2 format, chain DA [auth E] mmCIF format, chain HA [auth F] mmCIF format, chain RA [auth H] mmCIF format, chain P [auth A] mmCIF format, chain NA [auth G] mmCIF format, chain KB [auth L] mmCIF format, chain JB [auth L] mmCIF format, chain IB [auth L] mmCIF format, chain IA [auth F] mmCIF format, chain DA [auth E]	DA [auth E] HA [auth F] IA [auth F] IB [auth L] JB [auth L] DA [auth E], HA [auth F], IA [auth F], IB [auth L], JB [auth L], KB [auth L], NA [auth G], P [auth A], RA [auth H]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain IB [auth L] Focus chain JB [auth L] Focus chain KB [auth L] Focus chain NA [auth G] Focus chain P [auth A] Focus chain RA [auth H] Interactions & Density Focus chain DA [auth E] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain IB [auth L] Focus chain JB [auth L] Focus chain KB [auth L] Focus chain NA [auth G] Focus chain P [auth A] Focus chain RA [auth H]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain LA [auth G] SDF format, chain ZA [auth J] SDF format, chain Z [auth D] SDF format, chain YA [auth J] SDF format, chain Y [auth D] SDF format, chain UA [auth I] SDF format, chain U [auth C] SDF format, chain TA [auth I] SDF format, chain T [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain QA [auth H] SDF format, chain PA [auth H] SDF format, chain N [auth A] SDF format, chain MA [auth G] SDF format, chain M [auth A] SDF format, chain GB [auth L] SDF format, chain FB [auth L] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain DB [auth K] SDF format, chain CB [auth K] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain LA [auth G] MOL2 format, chain ZA [auth J] MOL2 format, chain Z [auth D] MOL2 format, chain YA [auth J] MOL2 format, chain Y [auth D] MOL2 format, chain UA [auth I] MOL2 format, chain U [auth C] MOL2 format, chain TA [auth I] MOL2 format, chain T [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth H] MOL2 format, chain PA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain GB [auth L] MOL2 format, chain FB [auth L] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain DB [auth K] MOL2 format, chain CB [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain LA [auth G] mmCIF format, chain ZA [auth J] mmCIF format, chain Z [auth D] mmCIF format, chain YA [auth J] mmCIF format, chain Y [auth D] mmCIF format, chain UA [auth I] mmCIF format, chain U [auth C] mmCIF format, chain TA [auth I] mmCIF format, chain T [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth H] mmCIF format, chain PA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain GB [auth L] mmCIF format, chain FB [auth L] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain DB [auth K] mmCIF format, chain CB [auth K] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] CB [auth K] DB [auth K] EA [auth F] BA [auth E], CA [auth E], CB [auth K], DB [auth K], EA [auth F], FA [auth F], FB [auth L], GB [auth L], LA [auth G], M [auth A], MA [auth G], N [auth A], PA [auth H], QA [auth H], R [auth B], S [auth B], T [auth C], TA [auth I], U [auth C], UA [auth I], Y [auth D], YA [auth J], Z [auth D], ZA [auth J]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain CB [auth K] Focus chain DB [auth K] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain FB [auth L] Focus chain GB [auth L] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain TA [auth I] Focus chain U [auth C] Focus chain UA [auth I] Focus chain Y [auth D] Focus chain YA [auth J] Focus chain Z [auth D] Focus chain ZA [auth J] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain CB [auth K] Focus chain DB [auth K] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain FB [auth L] Focus chain GB [auth L] Focus chain LA [auth G] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth C] Focus chain TA [auth I] Focus chain U [auth C] Focus chain UA [auth I] Focus chain Y [auth D] Focus chain YA [auth J] Focus chain Z [auth D] Focus chain ZA [auth J]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain OA [auth G] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain WA [auth I] MOL2 format, chain OA [auth G] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth I] mmCIF format, chain OA [auth G] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain WA [auth I]	OA [auth G], V [auth C], W [auth C], WA [auth I]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain OA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth I] Interactions & Density Focus chain OA [auth G] Focus chain V [auth C] Focus chain W [auth C] Focus chain WA [auth I]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain JA [auth F] SDF format, chain XA [auth I] SDF format, chain SA [auth H] SDF format, chain Q [auth A] SDF format, chain KA [auth F] SDF format, chain BB [auth J] MOL2 format, chain JA [auth F] MOL2 format, chain XA [auth I] MOL2 format, chain SA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain KA [auth F] MOL2 format, chain BB [auth J] mmCIF format, chain JA [auth F] mmCIF format, chain XA [auth I] mmCIF format, chain SA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain KA [auth F] mmCIF format, chain BB [auth J]	BB [auth J] JA [auth F] KA [auth F] Q [auth A] SA [auth H] BB [auth J], JA [auth F], KA [auth F], Q [auth A], SA [auth H], XA [auth I]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth J] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain Q [auth A] Focus chain SA [auth H] Focus chain XA [auth I] Interactions & Density Focus chain BB [auth J] Focus chain JA [auth F] Focus chain KA [auth F] Focus chain Q [auth A] Focus chain SA [auth H] Focus chain XA [auth I]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain VA [auth I] SDF format, chain HB [auth L] SDF format, chain GA [auth F] SDF format, chain EB [auth K] SDF format, chain AB [auth J] SDF format, chain AA [auth D] MOL2 format, chain VA [auth I] MOL2 format, chain HB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain EB [auth K] MOL2 format, chain AB [auth J] MOL2 format, chain AA [auth D] mmCIF format, chain VA [auth I] mmCIF format, chain HB [auth L] mmCIF format, chain GA [auth F] mmCIF format, chain EB [auth K] mmCIF format, chain AB [auth J] mmCIF format, chain AA [auth D]	AA [auth D] AB [auth J] EB [auth K] GA [auth F] HB [auth L] AA [auth D], AB [auth J], EB [auth K], GA [auth F], HB [auth L], VA [auth I]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain AB [auth J] Focus chain EB [auth K] Focus chain GA [auth F] Focus chain HB [auth L] Focus chain VA [auth I] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth J] Focus chain EB [auth K] Focus chain GA [auth F] Focus chain HB [auth L] Focus chain VA [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.218 (Depositor), 0.217 (DCC)
R-Value Work: 0.179 (Depositor), 0.180 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.518	α = 90
b = 308.038	β = 90.1
c = 97.167	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2019-03-06

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History (Full details and data files)

Version 1.0: 2019-03-06
Type: Initial release
Version 1.1: 2019-12-18
Changes: Author supporting evidence
Version 1.2: 2024-10-23
Changes: Data collection, Database references, Structure summary