3E6Q | pdb_00003e6q

Putative 5-carboxymethyl-2-hydroxymuconate isomerase from Pseudomonas aeruginosa.

PDB DOI: https://doi.org/10.2210/pdb3E6Q/pdb

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

Deposited: 2008-08-15 Released: 2008-08-26
Deposition Author(s): Osipiuk, J., Xu, X., Cui, H., Savchenko, A., Edwards, A.M., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.164 (Depositor), 0.168 (DCC)
R-Value Work:
0.136 (Depositor), 0.143 (DCC)
R-Value Observed:
0.137 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

X-ray crystal structure of putative 5-carboxymethyl-2-hydroxymuconate isomerase from Pseudomonas aeruginosa.

Osipiuk, J., Xu, X., Cui, H., Savchenko, A., Edwards, A.M., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 193.28 kDa
Atom Count: 14,344
Modeled Residue Count: 1,520
Deposited Residue Count: 1,752
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
putative 5-carboxymethyl-2-hydroxymuconate isomerase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	146	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: PA1966
UniProt
Find proteins for Q9I2D8 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9I2D8 Go to UniProtKB: Q9I2D8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9I2D8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain KA [auth H] SDF format, chain LA [auth H] SDF format, chain S [auth B] SDF format, chain WA [auth J] SDF format, chain X [auth C] SDF format, chain BA [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain KA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain S [auth B] MOL2 format, chain WA [auth J] MOL2 format, chain X [auth C] MOL2 format, chain BA [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain KA [auth H] mmCIF format, chain LA [auth H] mmCIF format, chain S [auth B] mmCIF format, chain WA [auth J] mmCIF format, chain X [auth C] mmCIF format, chain BA [auth E]	AA [auth E] BA [auth E] KA [auth H] LA [auth H] S [auth B] AA [auth E], BA [auth E], KA [auth H], LA [auth H], S [auth B], WA [auth J], X [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth E] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain S [auth B] Focus chain WA [auth J] Focus chain X [auth C] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth E] Focus chain KA [auth H] Focus chain LA [auth H] Focus chain S [auth B] Focus chain WA [auth J] Focus chain X [auth C]
IMD Query on IMD Download:Ideal Coordinates CCD File SDF format, chain YA [auth J] SDF format, chain FB [auth L] MOL2 format, chain YA [auth J] MOL2 format, chain FB [auth L] mmCIF format, chain YA [auth J] mmCIF format, chain FB [auth L]	FB [auth L], YA [auth J]	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Interactions Focus chain FB [auth L] Focus chain YA [auth J] Interactions & Density Focus chain FB [auth L] Focus chain YA [auth J]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain AB [auth K] SDF format, chain BB [auth K] SDF format, chain CA [auth E] SDF format, chain CB [auth L] SDF format, chain EA [auth F] SDF format, chain IA [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth H] SDF format, chain NA [auth H] SDF format, chain RA [auth I] SDF format, chain SA [auth I] SDF format, chain T [auth B] SDF format, chain TA [auth I] SDF format, chain XA [auth J] SDF format, chain Y [auth C] SDF format, chain Z [auth D] SDF format, chain ZA [auth K] MOL2 format, chain AB [auth K] MOL2 format, chain BB [auth K] MOL2 format, chain CA [auth E] MOL2 format, chain CB [auth L] MOL2 format, chain EA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain NA [auth H] MOL2 format, chain RA [auth I] MOL2 format, chain SA [auth I] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain XA [auth J] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth D] MOL2 format, chain ZA [auth K] mmCIF format, chain AB [auth K] mmCIF format, chain BB [auth K] mmCIF format, chain CA [auth E] mmCIF format, chain CB [auth L] mmCIF format, chain EA [auth F] mmCIF format, chain IA [auth G] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain NA [auth H] mmCIF format, chain RA [auth I] mmCIF format, chain SA [auth I] mmCIF format, chain T [auth B] mmCIF format, chain TA [auth I] mmCIF format, chain XA [auth J] mmCIF format, chain Y [auth C] mmCIF format, chain Z [auth D] mmCIF format, chain ZA [auth K]	AB [auth K] BB [auth K] CA [auth E] CB [auth L] EA [auth F] AB [auth K], BB [auth K], CA [auth E], CB [auth L], EA [auth F], IA [auth G], M [auth A], MA [auth H], NA [auth H], RA [auth I], SA [auth I], T [auth B], TA [auth I], XA [auth J], Y [auth C], Z [auth D], ZA [auth K]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain CB [auth L] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth I] Focus chain XA [auth J] Focus chain Y [auth C] Focus chain Z [auth D] Focus chain ZA [auth K] Interactions & Density Focus chain AB [auth K] Focus chain BB [auth K] Focus chain CA [auth E] Focus chain CB [auth L] Focus chain EA [auth F] Focus chain IA [auth G] Focus chain M [auth A] Focus chain MA [auth H] Focus chain NA [auth H] Focus chain RA [auth I] Focus chain SA [auth I] Focus chain T [auth B] Focus chain TA [auth I] Focus chain XA [auth J] Focus chain Y [auth C] Focus chain Z [auth D] Focus chain ZA [auth K]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain DA [auth E] SDF format, chain Q [auth A] MOL2 format, chain DA [auth E] MOL2 format, chain Q [auth A] mmCIF format, chain DA [auth E] mmCIF format, chain Q [auth A]	DA [auth E], Q [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain DA [auth E] Focus chain Q [auth A] Interactions & Density Focus chain DA [auth E] Focus chain Q [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain EB [auth L] SDF format, chain FA [auth F] SDF format, chain GA [auth F] SDF format, chain GB [auth L] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth H] SDF format, chain QA [auth H] SDF format, chain UA [auth I] SDF format, chain VA [auth I] SDF format, chain W [auth B] SDF format, chain U [auth B] SDF format, chain OA [auth H] SDF format, chain DB [auth L] MOL2 format, chain EB [auth L] MOL2 format, chain FA [auth F] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth L] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth H] MOL2 format, chain QA [auth H] MOL2 format, chain UA [auth I] MOL2 format, chain VA [auth I] MOL2 format, chain W [auth B] MOL2 format, chain U [auth B] MOL2 format, chain OA [auth H] MOL2 format, chain DB [auth L] mmCIF format, chain EB [auth L] mmCIF format, chain FA [auth F] mmCIF format, chain GA [auth F] mmCIF format, chain GB [auth L] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth H] mmCIF format, chain QA [auth H] mmCIF format, chain UA [auth I] mmCIF format, chain VA [auth I] mmCIF format, chain W [auth B] mmCIF format, chain U [auth B] mmCIF format, chain OA [auth H] mmCIF format, chain DB [auth L]	DB [auth L] EB [auth L] FA [auth F] GA [auth F] GB [auth L] DB [auth L], EB [auth L], FA [auth F], GA [auth F], GB [auth L], N [auth A], O [auth A], OA [auth H], P [auth A], PA [auth H], QA [auth H], U [auth B], UA [auth I], VA [auth I], W [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain DB [auth L] Focus chain EB [auth L] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain U [auth B] Focus chain UA [auth I] Focus chain VA [auth I] Focus chain W [auth B] Interactions & Density Focus chain DB [auth L] Focus chain EB [auth L] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth H] Focus chain P [auth A] Focus chain PA [auth H] Focus chain QA [auth H] Focus chain U [auth B] Focus chain UA [auth I] Focus chain VA [auth I] Focus chain W [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain HA [auth F] SDF format, chain JA [auth G] SDF format, chain R [auth A] SDF format, chain V [auth B] MOL2 format, chain HA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain R [auth A] MOL2 format, chain V [auth B] mmCIF format, chain HA [auth F] mmCIF format, chain JA [auth G] mmCIF format, chain R [auth A] mmCIF format, chain V [auth B]	HA [auth F], JA [auth G], R [auth A], V [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain HA [auth F] Focus chain JA [auth G] Focus chain R [auth A] Focus chain V [auth B] Interactions & Density Focus chain HA [auth F] Focus chain JA [auth G] Focus chain R [auth A] Focus chain V [auth B]

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: 1.75 Å
R-Value Free: 0.164 (Depositor), 0.168 (DCC)
R-Value Work: 0.136 (Depositor), 0.143 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 172.796	α = 90
b = 145.243	β = 134.91
c = 122.252	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-3000	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2008-08-26

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2008-08-26
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2020-05-13
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-11-06
Changes: Data collection, Database references, Derived calculations, Structure summary