5I28 | pdb_00005i28

Azurin T30R1, crystal form II

PDB DOI: https://doi.org/10.2210/pdb5I28/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Pseudomonas aeruginosa
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2016-02-08 Released: 2016-04-13
Deposition Author(s): Hagelueken, G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free:
0.271 (Depositor), 0.271 (DCC)
R-Value Work:
0.212 (Depositor), 0.213 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Determination of nitroxide spin label conformations via PELDOR and X-ray crystallography.

Abdullin, D., Hagelueken, G., Schiemann, O.

(2016) Phys Chem Chem Phys 18: 10428-10437

PubMed: 27029516 Search on PubMed
DOI: https://doi.org/10.1039/c6cp01307d
Primary Citation Related Structures:
5I26, 5I28

PubMed Abstract:
Pulsed electron-electron double resonance (PELDOR or DEER) in combination with site-directed spin labelling has emerged as an important method for measuring nanometer distance constraints that are used to obtain coarse-grained structures of biomolecules or to follow their conformational changes. Translating measured spin-spin distances between spin labels into structural information requires taking the conformational flexibility of spin label side chains into account. Here, we present an analysis of orientation selective PELDOR data recorded on six singly MTSSL-labelled azurin mutants. The analysis yielded conformational MTSSL ensembles, which are considerably narrower than those predicted using in silico spin labeling methods but match well with spin label conformations found in the corresponding crystal structures. The possible reasons and consequences for predicting spin label conformers in the fold of biomolecules are discussed.

Organizational Affiliation

Institute of Physical and Theoretical Chemistry, University of Bonn, Wegelerstr. 12, 53115 Bonn, Germany. schiemann@pc.uni-bonn.de.

Macromolecule Content

Total Structure Weight: 227.48 kDa
Atom Count: 17,003
Modeled Residue Count: 2,048
Deposited Residue Count: 2,048
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, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	128	Pseudomonas aeruginosa	Mutation(s): 1 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain R [auth A] MOL2 format, chain R [auth A] mmCIF format, chain R [auth A]	R [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain R [auth A] Interactions & Density Focus chain R [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain Y [auth H] SDF format, chain X [auth G] SDF format, chain W [auth F] SDF format, chain V [auth E] SDF format, chain U [auth D] SDF format, chain T [auth C] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain GA [auth P] SDF format, chain FA [auth O] SDF format, chain EA [auth N] SDF format, chain DA [auth M] SDF format, chain CA [auth L] SDF format, chain BA [auth K] SDF format, chain AA [auth J] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth G] MOL2 format, chain W [auth F] MOL2 format, chain V [auth E] MOL2 format, chain U [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain GA [auth P] MOL2 format, chain FA [auth O] MOL2 format, chain EA [auth N] MOL2 format, chain DA [auth M] MOL2 format, chain CA [auth L] MOL2 format, chain BA [auth K] MOL2 format, chain AA [auth J] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth G] mmCIF format, chain W [auth F] mmCIF format, chain V [auth E] mmCIF format, chain U [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain GA [auth P] mmCIF format, chain FA [auth O] mmCIF format, chain EA [auth N] mmCIF format, chain DA [auth M] mmCIF format, chain CA [auth L] mmCIF format, chain BA [auth K] mmCIF format, chain AA [auth J]	AA [auth J] BA [auth K] CA [auth L] DA [auth M] EA [auth N] AA [auth J], BA [auth K], CA [auth L], DA [auth M], EA [auth N], FA [auth O], GA [auth P], Q [auth A], S [auth B], T [auth C], U [auth D], V [auth E], W [auth F], X [auth G], Y [auth H], Z [auth I]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth O] Focus chain GA [auth P] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth K] Focus chain CA [auth L] Focus chain DA [auth M] Focus chain EA [auth N] Focus chain FA [auth O] Focus chain GA [auth P] Focus chain Q [auth A] Focus chain S [auth B] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth E] Focus chain W [auth F] Focus chain X [auth G] Focus chain Y [auth H] Focus chain Z [auth I]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
R1A Query on R1A	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	L-PEPTIDE LINKING	C₁₂ H₂₁ N₂ O₃ S₂		CYS

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.271 (Depositor), 0.271 (DCC)
R-Value Work: 0.212 (Depositor), 0.213 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 242.478	α = 90
b = 105.56	β = 114.42
c = 100.051	γ = 90

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2016-04-13

Deposition Author(s):

Hagelueken, G.

Revision History (Full details and data files)

Version 1.0: 2016-04-13
Type: Initial release
Version 1.1: 2016-04-20
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description