2Z68 | pdb_00002z68

Crystal Structure Of An Artificial Metalloprotein: Cr[N-salicylidene-4-amino-3-hydroxyhydrocinnamic acid]/Wild Type Heme oxygenase

PDB DOI: https://doi.org/10.2210/pdb2Z68/pdb

Classification: OXIDOREDUCTASE
Organism(s): Corynebacterium diphtheriae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-07-24 Released: 2007-08-28
Deposition Author(s): Yokoi, N., Unno, M., Ueno, T., Ikeda-Saito, M., Watanabe, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free:
0.225 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.175 (DCC)
R-Value Observed:
0.180 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Ligand design for the improvement of stability of metal complex.protein hybrids.

Yokoi, N., Ueno, T., Unno, M., Matsui, T., Ikeda-Saito, M., Watanabe, Y.

(2008) Chem Commun (Camb) : 229-231

PubMed: 18092096 Search on PubMed
DOI: https://doi.org/10.1039/b713468a
Primary Citation Related Structures:
2Z68

PubMed Abstract:
We have succeeded in improving the stability of Fe(Schiff-base).heme oxygenase (HO) hybrids by ligand design based on the crystal structure of Fe(N,N'-bis(salicylidene)-3.4-diaminobenzene propionic acid).HO.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8602, Japan.

Macromolecule Content

Total Structure Weight: 49.35 kDa
Atom Count: 3,802
Modeled Residue Count: 417
Deposited Residue Count: 430
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heme oxygenase	A, B	215	Corynebacterium diphtheriae	Mutation(s): 0 EC: 1.14.99.3 (PDB Primary Data), 1.14.14.18 (UniProt)
UniProt
Find proteins for Q54AI1 (Corynebacterium diphtheriae) Explore Q54AI1 Go to UniProtKB: Q54AI1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q54AI1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TIL Query on TIL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	F [auth A], I [auth B]	[2-[5-CARBOXYETHYL-2-PHENOLATO(NITRILOMETHYLIDYNE)][PHENOLATO]]CHROMIUM(III) C₁₆ H₁₃ Cr N O₄ PQEURDOLYHRQIK-LZMXEPDESA-L		Interactions Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain F [auth A] Focus chain I [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain G [auth B]	C [auth A], D [auth A], G [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain G [auth B]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.58 Å
R-Value Free: 0.225 (Depositor), 0.220 (DCC)
R-Value Work: 0.178 (Depositor), 0.175 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.656	α = 90
b = 63.057	β = 96.88
c = 77.964	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
X-PLOR	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-08-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2007-08-28
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-09-18
Changes: Database references