2UYD

Crystal structure of the SmHasA mutant H83A

PDB DOI: https://doi.org/10.2210/pdb2UYD/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Serratia marcescens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-04 Released: 2007-12-25
Deposition Author(s): Czjzek, M., Caillet-Saguy, C., Fournelle, A., Guigliarelli, B., Izadi-Pruneyre, N., Lecroisey, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.274 (Depositor), 0.300 (DCC)
R-Value Work:
0.236 (Depositor), 0.260 (DCC)
R-Value Observed:
0.238 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Deciphering the Structural Role of Histidine 83 for Heme Binding in Hemophore Hasa.

Caillet-Saguy, C., Turano, P., Piccioli, M., Lukat-Rodgers, G.S., Czjzek, M., Guigliarelli, B., Izadi-Pruneyre, N., Rodgers, K.R., Delepierre, M., Lecroisey, A.

(2008) J Biol Chem 283: 5960

PubMed: 18162469 Search on PubMed
DOI: https://doi.org/10.1074/jbc.M703795200
Primary Citation of Related Structures:
2UYD

PubMed Abstract:
Heme carrier HasA has a unique type of histidine/tyrosine heme iron ligation in which the iron ion is in a thermally driven two spin states equilibrium. We recently suggested that the H-bonding between Tyr75 and the invariantly conserved residue His83 modulates the strength of the iron-Tyr75 bond. To unravel the role of His83, we characterize the iron ligation and the electronic properties of both wild type and H83A mutant by a variety of spectroscopic techniques. Although His83 in wild type modulates the strength of the Tyr-iron bond, its removal causes detachment of the tyrosine ligand, thus giving rise to a series of pH-dependent equilibria among species with different axial ligation. The five coordinated species detected at physiological pH may represent a possible intermediate of the heme transfer mechanism to the receptor.

Organizational Affiliation

Unité de RMN des Biomolécules, CNRS URA 2185, Institut Pasteur, 75015 Paris, France. ccaillet@pasteur.fr

Macromolecule Content

Total Structure Weight: 20.48 kDa
Atom Count: 1,430
Modelled Residue Count: 175
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEMOPHORE HASA	A [auth X]	188	Serratia marcescens	Mutation(s): 1
UniProt
Find proteins for Q54450 (Serratia marcescens) Explore Q54450 Go to UniProtKB: Q54450
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q54450
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth X] SDF format, chain E [auth X] SDF format, chain F [auth X] SDF format, chain G [auth X] SDF format, chain H [auth X] SDF format, chain I [auth X] SDF format, chain J [auth X] MOL2 format, chain C [auth X] MOL2 format, chain D [auth X] MOL2 format, chain E [auth X] MOL2 format, chain F [auth X] MOL2 format, chain G [auth X] MOL2 format, chain H [auth X] MOL2 format, chain I [auth X] MOL2 format, chain J [auth X] mmCIF format, chain C [auth X] mmCIF format, chain D [auth X] mmCIF format, chain E [auth X] mmCIF format, chain F [auth X] mmCIF format, chain G [auth X] mmCIF format, chain H [auth X] mmCIF format, chain I [auth X] mmCIF format, chain J [auth X]	C [auth X] D [auth X] E [auth X] F [auth X] G [auth X] C [auth X], D [auth X], E [auth X], F [auth X], G [auth X], H [auth X], I [auth X], J [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X] Interactions & Density Focus chain C [auth X] Focus chain D [auth X] Focus chain E [auth X] Focus chain F [auth X] Focus chain G [auth X] Focus chain H [auth X] Focus chain I [auth X] Focus chain J [auth X]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain K [auth X] SDF format, chain L [auth X] MOL2 format, chain K [auth X] MOL2 format, chain L [auth X] mmCIF format, chain K [auth X] mmCIF format, chain L [auth X]	K [auth X], L [auth X]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain K [auth X] Focus chain L [auth X] Interactions & Density Focus chain K [auth X] Focus chain L [auth X]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.274 (Depositor), 0.300 (DCC)
R-Value Work: 0.236 (Depositor), 0.260 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.67	α = 90
b = 110.67	β = 90
c = 52.355	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-12-25

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-12-25
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-05-08
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Derived calculations, Other, Refinement description