5YT7 | pdb_00005yt7

crystal structure of circularly permutated Azurin 3

PDB DOI: https://doi.org/10.2210/pdb5YT7/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa PAO1
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2017-11-17 Released: 2018-08-08
Deposition Author(s): Chen, H.H., Liu, H.P., Yu, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free:
0.217 (Depositor), 0.226 (DCC)
R-Value Work:
0.162 (Depositor), 0.173 (DCC)
R-Value Observed:
0.164 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Engineering the Metal-binding Loop of a Blue Copper Protein by Circular Permutation

Chen, H.H., Su, B., Zhang, T.T., Huang, A., Liu, H.P., Yu, Y., Wang, J.

(2017) RSC Adv : 56093-56098

DOI: https://doi.org/10.1039/C7RA11512A

Macromolecule Content

Total Structure Weight: 58.27 kDa
Atom Count: 4,557
Modeled Residue Count: 528
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Azurin	A, B, C, D	133	Pseudomonas aeruginosa PAO1	Mutation(s): 0 Gene Names: azu, PA4922
UniProt
Find proteins for P00282 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore P00282 Go to UniProtKB: P00282
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P00282
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] SDF format, chain Q [auth C] SDF format, chain T [auth D] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth D] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain T [auth D]	E [auth A], K [auth B], Q [auth C], T [auth D]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain K [auth B] Focus chain Q [auth C] Focus chain T [auth D]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain R [auth C] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain R [auth C] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain R [auth C]	G [auth A], N [auth B], O [auth B], R [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain R [auth C]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain F [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain F [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	F [auth A], L [auth B], M [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain F [auth A] Focus chain L [auth B] Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain P [auth B] MOL2 format, chain H [auth A] MOL2 format, chain P [auth B] mmCIF format, chain H [auth A] mmCIF format, chain P [auth B]	H [auth A], P [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain H [auth A] Focus chain P [auth B] Interactions & Density Focus chain H [auth A] Focus chain P [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain S [auth C] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain S [auth C] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain S [auth C]	I [auth A], J [auth A], S [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth C] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain S [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.66 Å
R-Value Free: 0.217 (Depositor), 0.226 (DCC)
R-Value Work: 0.162 (Depositor), 0.173 (DCC)
R-Value Observed: 0.164 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.888	α = 90
b = 87.968	β = 110.22
c = 66.096	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2018-08-08

Deposition Author(s):

Chen, H.H.

Liu, H.P.

Yu, Y.

Revision History (Full details and data files)

Version 1.0: 2018-08-08
Type: Initial release
Version 1.1: 2024-11-13
Changes: Data collection, Database references, Derived calculations, Structure summary