3ZYB

CRYSTAL STRUCTURE OF PA-IL LECTIN COMPLEXED WITH GALAG0 AT 2.3 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3ZYB/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2011-08-19 Released: 2011-09-21
Deposition Author(s): Kadam, R.U., Bergmann, M., Hurley, M., Garg, D., Cacciarini, M., Swiderska, M.A., Nativi, C., Sattler, M., Smyth, A.R., Williams, P., Camara, M., Stocker, A., Darbre, T., Reymond, J.-L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.240
R-Value Work: 0.214
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 107.14 kDa
Atom Count: 8,394
Modelled Residue Count: 980
Deposited Residue Count: 988
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PA-I galactophilic lectin	A, B, C, D, E A, B, C, D, E, F, G, H	122	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: lecA, pa1L, PA2570
UniProt
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q05097 Go to UniProtKB: Q05097
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q05097
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GALA-LYS-PRO-LEUNH2	I, J, K [auth N]	4	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAL Query on GAL Download Ideal Coordinates CCD File SDF format, chain BA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain M [auth A] SDF format, chain P [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] SDF format, chain Y [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain M [auth A] MOL2 format, chain P [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D] MOL2 format, chain Y [auth E]	BA [auth F] EA [auth G] HA [auth H] M [auth A] P [auth B] BA [auth F], EA [auth G], HA [auth H], M [auth A], P [auth B], S [auth C], V [auth D], Y [auth E]	beta-D-galactopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-FPRJBGLDSA-N		Interactions Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E] Interactions & Density Focus chain BA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain M [auth A] Focus chain P [auth B] Focus chain S [auth C] Focus chain V [auth D] Focus chain Y [auth E]
PHB Query on PHB Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain FA [auth G] SDF format, chain IA [auth H] SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain IA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain Z [auth E]	CA [auth F] FA [auth G] IA [auth H] N [auth A] Q [auth B] CA [auth F], FA [auth G], IA [auth H], N [auth A], Q [auth B], T [auth C], W [auth D], Z [auth E]	P-HYDROXYBENZOIC ACID C₇ H₆ O₃ FJKROLUGYXJWQN-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain FA [auth G] Focus chain IA [auth H] Focus chain N [auth A] Focus chain Q [auth B] Focus chain T [auth C] Focus chain W [auth D] Focus chain Z [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain DA [auth G] SDF format, chain GA [auth H] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain R [auth C] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain GA [auth H] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E]	AA [auth F] DA [auth G] GA [auth H] L [auth A] O [auth B] AA [auth F], DA [auth G], GA [auth H], L [auth A], O [auth B], R [auth C], U [auth D], X [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain AA [auth F] Focus chain DA [auth G] Focus chain GA [auth H] Focus chain L [auth A] Focus chain O [auth B] Focus chain R [auth C] Focus chain U [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.29 Å
R-Value Free: 0.240
R-Value Work: 0.214
R-Value Observed: 0.215
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.332	α = 90
b = 128.559	β = 90
c = 146.063	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-09-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-09-21
Type: Initial release
Version 1.1: 2012-04-25
Changes: Other
Version 1.2: 2017-02-08
Changes: Source and taxonomy
Version 1.3: 2017-07-12
Changes: Derived calculations
Version 1.4: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary
Version 1.5: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary