3C8O | pdb_00003c8o

The Crystal Structure of RraA from PAO1

PDB DOI: https://doi.org/10.2210/pdb3C8O/pdb

Classification: HYDROLASE REGULATOR
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2008-02-12 Released: 2009-02-17
Deposition Author(s): Luo, M., Niu, S., Yin, Y., Huang, A., Wang, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.249 (Depositor), 0.243 (DCC)
R-Value Work:
0.221 (Depositor), 0.216 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

The Crystal Structure of RraA from PAO1

Luo, M., Niu, S., Yin, Y., Huang, A., Wang, D.

To be published.

Macromolecule Content

Total Structure Weight: 39.35 kDa
Atom Count: 2,855
Modeled Residue Count: 321
Deposited Residue Count: 324
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Regulator of ribonuclease activity A	A, B	162	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: rraA EC: 4.1.3.17 (UniProt), 4.1.1.112 (UniProt)
UniProt
Find proteins for Q9I2W7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I2W7 Go to UniProtKB: Q9I2W7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I2W7
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PG4 Query on PG4 Download:Ideal Coordinates CCD File SDF format, chain CB [auth B] MOL2 format, chain CB [auth B] mmCIF format, chain CB [auth B]	CB [auth B]	TETRAETHYLENE GLYCOL C₈ H₁₈ O₅ UWHCKJMYHZGTIT-UHFFFAOYSA-N		Interactions Focus chain CB [auth B] Interactions & Density Focus chain CB [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain ZA [auth B] SDF format, chain X [auth A] SDF format, chain BB [auth B] SDF format, chain AB [auth B] MOL2 format, chain ZA [auth B] MOL2 format, chain X [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain AB [auth B] mmCIF format, chain ZA [auth B] mmCIF format, chain X [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain AB [auth B]	AB [auth B], BB [auth B], X [auth A], ZA [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AB [auth B] Focus chain BB [auth B] Focus chain X [auth A] Focus chain ZA [auth B] Interactions & Density Focus chain AB [auth B] Focus chain BB [auth B] Focus chain X [auth A] Focus chain ZA [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain EA [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain GB [auth B] SDF format, chain FB [auth B] SDF format, chain EB [auth B] SDF format, chain DB [auth B] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain BA [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain GB [auth B] MOL2 format, chain FB [auth B] MOL2 format, chain EB [auth B] MOL2 format, chain DB [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain BA [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain GB [auth B] mmCIF format, chain FB [auth B] mmCIF format, chain EB [auth B] mmCIF format, chain DB [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain BA [auth A]	AA [auth A] BA [auth A] CA [auth A] DA [auth A] DB [auth B] AA [auth A], BA [auth A], CA [auth A], DA [auth A], DB [auth B], EA [auth A], EB [auth B], FB [auth B], GB [auth B], Y [auth A], Z [auth A]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain CA [auth A] Focus chain DA [auth A] Focus chain DB [auth B] Focus chain EA [auth A] Focus chain EB [auth B] Focus chain FB [auth B] Focus chain GB [auth B] Focus chain Y [auth A] Focus chain Z [auth A]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain LA [auth B] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain OA [auth B] SDF format, chain PA [auth B] SDF format, chain QA [auth B] SDF format, chain R [auth A] SDF format, chain RA [auth B] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain W [auth A] SDF format, chain YA [auth B] SDF format, chain XA [auth B] SDF format, chain WA [auth B] SDF format, chain UA [auth B] SDF format, chain U [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain MA [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain KA [auth B] SDF format, chain K [auth A] SDF format, chain JA [auth B] SDF format, chain IA [auth B] SDF format, chain HA [auth B] SDF format, chain GA [auth B] SDF format, chain FA [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain OA [auth B] MOL2 format, chain PA [auth B] MOL2 format, chain QA [auth B] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth B] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain XA [auth B] MOL2 format, chain WA [auth B] MOL2 format, chain UA [auth B] MOL2 format, chain U [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth B] MOL2 format, chain HA [auth B] MOL2 format, chain GA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain OA [auth B] mmCIF format, chain PA [auth B] mmCIF format, chain QA [auth B] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth B] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain XA [auth B] mmCIF format, chain WA [auth B] mmCIF format, chain UA [auth B] mmCIF format, chain U [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth B] mmCIF format, chain HA [auth B] mmCIF format, chain GA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] FA [auth B] C [auth A], D [auth A], E [auth A], F [auth A], FA [auth B], G [auth A], GA [auth B], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], K [auth A], KA [auth B], L [auth A], LA [auth B], M [auth A], MA [auth B], N [auth A], NA [auth B], O [auth A], OA [auth B], P [auth A], PA [auth B], Q [auth A], QA [auth B], R [auth A], RA [auth B], S [auth A], SA [auth B], T [auth A], TA [auth B], U [auth A], UA [auth B], V [auth A], VA [auth B], W [auth A], WA [auth B], XA [auth B], YA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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 FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [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 FA [auth B] Focus chain G [auth A] Focus chain GA [auth B] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain K [auth A] Focus chain KA [auth B] Focus chain L [auth A] Focus chain LA [auth B] Focus chain M [auth A] Focus chain MA [auth B] Focus chain N [auth A] Focus chain NA [auth B] Focus chain O [auth A] Focus chain OA [auth B] Focus chain P [auth A] Focus chain PA [auth B] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain R [auth A] Focus chain RA [auth B] Focus chain S [auth A] Focus chain SA [auth B] Focus chain T [auth A] Focus chain TA [auth B] Focus chain U [auth A] Focus chain UA [auth B] Focus chain V [auth A] Focus chain VA [auth B] Focus chain W [auth A] Focus chain WA [auth B] Focus chain XA [auth B] Focus chain YA [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.249 (Depositor), 0.243 (DCC)
R-Value Work: 0.221 (Depositor), 0.216 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.679	α = 90
b = 98.679	β = 90
c = 180.26	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
AUTOMAR	data reduction
AMoRE	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-02-17

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-02-17
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2019-12-04
Changes: Advisory, Data collection
Version 1.3: 2023-11-01
Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description