1VB6 | pdb_00001vb6

Crystal Structure of the heme PAS sensor domain of Ec DOS (oxygen-bound form)

PDB DOI: https://doi.org/10.2210/pdb1VB6/pdb

Classification: SIGNALING PROTEIN
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2004-02-24 Released: 2005-04-19
Deposition Author(s): Kurokawa, H., Watanabe, M., Sagami, I., Mikami, B., Shimizu, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free:
0.232 (Depositor), 0.220 (DCC)
R-Value Work:
0.214 (Depositor), 0.200 (DCC)
R-Value Observed:
0.214 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure of oxygen-bound form of a Heme PAS domain of Ec DOS

Kurokawa, H., Watanabe, M., Sagami, I., Mikami, B., Shimizu, T.

To be published.

Macromolecule Content

Total Structure Weight: 39.31 kDa
Atom Count: 2,199
Modelled Residue Count: 224
Deposited Residue Count: 334
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme pas sensor protein	A, B	167	Escherichia coli K-12	Mutation(s): 0 EC: 3.1.4.52
UniProt
Find proteins for P76129 (Escherichia coli (strain K12)) Explore P76129 Go to UniProtKB: P76129
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P76129
Sequence Annotations Expand
Reference Sequence LOADING

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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
OXY Query on OXY Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	OXYGEN MOLECULE O₂ MYMOFIZGZYHOMD-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.56 Å
R-Value Free: 0.232 (Depositor), 0.220 (DCC)
R-Value Work: 0.214 (Depositor), 0.200 (DCC)
R-Value Observed: 0.214 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.894	α = 90
b = 69.337	β = 90
c = 81.876	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2005-04-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-19
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal Structure of the heme PAS sensor domain of Ec DOS (oxygen-bound form)

Structure of oxygen-bound form of a Heme PAS domain of Ec DOS

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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