3KBR | pdb_00003kbr

The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01

PDB DOI: https://doi.org/10.2210/pdb3KBR/pdb

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

Deposited: 2009-10-20 Released: 2009-11-10
Deposition Author(s): Tan, K., Marshall, N., Buck, K., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.213 (Depositor), 0.209 (DCC)
R-Value Work:
0.183 (Depositor), 0.178 (DCC)
R-Value Observed:
0.184 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01

Tan, K., Marshall, N., Buck, K., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 28.52 kDa
Atom Count: 2,133
Modeled Residue Count: 231
Deposited Residue Count: 239
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclohexadienyl dehydratase	A	239	Pseudomonas aeruginosa	Mutation(s): 0 Gene Names: PA3475, pheC, Pseudomonas aeruginosa EC: 4.2.1.51 (PDB Primary Data), 4.2.1.91 (PDB Primary Data)
UniProt
Find proteins for Q01269 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q01269 Go to UniProtKB: Q01269
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q01269
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain K [auth A] MOL2 format, chain K [auth A] mmCIF format, chain K [auth A]	K [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Interactions & Density Focus chain K [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A]	D [auth A], E [auth A], F [auth A], H [auth A], I [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A]
NI Query on NI Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A]	G [auth A], J [auth A]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.213 (Depositor), 0.209 (DCC)
R-Value Work: 0.183 (Depositor), 0.178 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.39	α = 90
b = 126.39	β = 90
c = 88.981	γ = 120

Software Package:

Software Name	Purpose
SBC-Collect	data collection
SHELXD	phasing
MLPHARE	phasing
DM	model building
ARP	model building
WARP	model building
HKL-3000	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
DM	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-11-10

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2009-11-10
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2024-10-09
Changes: Data collection, Database references, Derived calculations, Structure summary

3KBR | pdb_00003kbr

The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01

Literature

The crystal structure of cyclohexadienyl dehydratase precursor from Pseudomonas aeruginosa PA01

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)