8VGU | pdb_00008vgu

Crystal structure of BcTSPO/Hematin complex

PDB DOI: https://doi.org/10.2210/pdb8VGU/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Bacillus cereus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-12-28 Released: 2025-01-15
Deposition Author(s): Qiu, W., Guo, Y., Hendrickson, W.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.253 (Depositor), 0.255 (DCC)
R-Value Work:
0.218 (Depositor), 0.229 (DCC)
R-Value Observed:
0.220 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of BcTSPO complexed with hematin

Qiu, W., Guo, Y., Hendrickson, W.A.

(null) Pnas

Macromolecule Content

Total Structure Weight: 47.15 kDa
Atom Count: 2,708
Modeled Residue Count: 302
Deposited Residue Count: 362
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tryptophan-rich protein TspO	A, B	181	Bacillus cereus	Mutation(s): 0 Gene Names: BW896_26980
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MH0 (Subject of Investigation/LOI) Query on MH0 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain H [auth B] MOL2 format, chain C [auth A] MOL2 format, chain H [auth B] mmCIF format, chain C [auth A] mmCIF format, chain H [auth B]	C [auth A], H [auth B]	Mesoheme C₃₄ H₃₆ Fe N₄ O₄ CKMCSMAXNUVLQI-RGGAHWMASA-N		Interactions Focus chain C [auth A] Focus chain H [auth B] Interactions & Density Focus chain C [auth A] Focus chain H [auth B]
MPG (Subject of Investigation/LOI) Query on MPG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B]	D [auth A] E [auth A] F [auth A] I [auth B] J [auth B] D [auth A], E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], L [auth B], M [auth B]	[(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate C₂₁ H₄₀ O₄ JPJYKWFFJCWMPK-GDCKJWNLSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
OXY (Subject of Investigation/LOI) Query on OXY Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain N [auth B] MOL2 format, chain G [auth A] MOL2 format, chain N [auth B] mmCIF format, chain G [auth A] mmCIF format, chain N [auth B]	G [auth A], N [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain N [auth B] Interactions & Density Focus chain G [auth A] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.253 (Depositor), 0.255 (DCC)
R-Value Work: 0.218 (Depositor), 0.229 (DCC)
R-Value Observed: 0.220 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.523	α = 90
b = 46.983	β = 92.28
c = 67.853	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-01-15

Deposition Author(s):

Qiu, W.

Guo, Y.

Hendrickson, W.A.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM107462
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM116799