4JET | pdb_00004jet

2.2A resolution structure of Holo hemophore HasA from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb4JET/pdb

Classification: HEME BINDING PROTEIN, TRANSPORT PROTEIN
Organism(s): Yersinia pestis
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-02-27 Released: 2013-04-24
Deposition Author(s): Kumar, R., Lovell, S., Battaile, K.P., Rivera, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.223 (Depositor), 0.228 (DCC)
R-Value Work:
0.166 (Depositor), 0.177 (DCC)
R-Value Observed:
0.169 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

The Hemophore HasA from Yersinia pestis (HasAyp) Coordinates Hemin with a Single Residue, Tyr75, and with Minimal Conformational Change.

Kumar, R., Lovell, S., Matsumura, H., Battaile, K.P., Moenne-Loccoz, P., Rivera, M.

(2013) Biochemistry 52: 2705-2707

PubMed: 23578210 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1021/bi400280z
Primary Citation Related Structures:
4JER, 4JES, 4JET

PubMed Abstract:
Hemophores from Serratia marcescens (HasA(sm)) and Pseudomonas aeruginosa (HasA(p)) bind hemin between two loops, which harbor the axial ligands H32 and Y75. Hemin binding to the Y75 loop triggers closing of the H32 loop and enables binding of H32. Because Yersinia pestis HasA (HasA(yp)) presents a Gln at position 32, we determined the structures of apo- and holo-HasA(yp). Surprisingly, the Q32 loop in apo-HasA(yp) is already in the closed conformation, but no residue from the Q32 loop binds hemin in holo-HasA(yp). In agreement with the minimal reorganization between the apo- and holo-structures, the hemin on-rate is too fast to detect by conventional stopped-flow measurements.

Organizational Affiliation

Center for Bioinformatics, University of Kansas, 2030 Becker Drive, Lawrence, KS 66047, USA.

Macromolecule Content

Total Structure Weight: 216.77 kDa
Atom Count: 14,784
Modeled Residue Count: 1,789
Deposited Residue Count: 1,930
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemophore HasA	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	193	Yersinia pestis	Mutation(s): 0 Gene Names: hasA, y0314, YP_3127, YPO3922
UniProt
Find proteins for Q0WA92 (Yersinia pestis) Explore Q0WA92 Go to UniProtKB: Q0WA92
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q0WA92
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain CA [auth J] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain O [auth C] SDF format, chain Q [auth D] SDF format, chain S [auth E] SDF format, chain U [auth F] SDF format, chain Y [auth H] SDF format, chain W [auth G] MOL2 format, chain AA [auth I] MOL2 format, chain CA [auth J] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F] MOL2 format, chain Y [auth H] MOL2 format, chain W [auth G] mmCIF format, chain AA [auth I] mmCIF format, chain CA [auth J] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain S [auth E] mmCIF format, chain U [auth F] mmCIF format, chain Y [auth H] mmCIF format, chain W [auth G]	AA [auth I] CA [auth J] K [auth A] M [auth B] O [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], O [auth C], Q [auth D], S [auth E], U [auth F], W [auth G], Y [auth H]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain O [auth C] Focus chain Q [auth D] Focus chain S [auth E] Focus chain U [auth F] Focus chain W [auth G] Focus chain Y [auth H]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain DA [auth J] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain R [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Z [auth H] MOL2 format, chain BA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Z [auth H] mmCIF format, chain BA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Z [auth H]	BA [auth I] DA [auth J] L [auth A] N [auth B] P [auth C] BA [auth I], DA [auth J], L [auth A], N [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Z [auth H]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.223 (Depositor), 0.228 (DCC)
R-Value Work: 0.166 (Depositor), 0.177 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.369	α = 90
b = 69.559	β = 100.12
c = 232.317	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2013-04-24

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-24
Type: Initial release
Version 1.1: 2013-05-29
Changes: Database references
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

4JET | pdb_00004jet

2.2A resolution structure of Holo hemophore HasA from Yersinia pestis

Literature

The Hemophore HasA from Yersinia pestis (HasAyp) Coordinates Hemin with a Single Residue, Tyr75, and with Minimal Conformational Change.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Biological Assembly 6

Biological Assembly 7

Biological Assembly 8

Biological Assembly 9

Biological Assembly 10

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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