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BMRB: 50269

4QGN

Fe+2-containing acireductone dioxygenase (Homo sapiens)

Authors

Pochapsky, T.C., Deshpande, A., Liu, X.

Assembly

acireductone dioxygenase

Entity

1. acireductone dioxygenase, entity 1 (polymer, Thiol state: all free), 179 monomers, 21498.13 Da Detail

MVQAWYMDDA PGDPRQPHRP DPGRPVGLEQ LRRLGVLYWK LDADKYENDP ELEKIRRERN YSWMDIITIC KDKLPNYEEK IKMFYEEHLH LDDEIRYILD GSGYFDVRDK EDQWIRIFME KGDMVTLPAG IYHRFTVDEK NYTKAMRLFV GEPVWTAYNR PADHFEARGQ YVKFLAQTA

2. acireductone dioxygenase, entity FE2 (non-polymer), 55.845 Da

Total weight

21553.977 Da

Max. entity weight

21498.13 Da

Entity Connection

ID	Type	Value order	Atom ID 1	Atom ID 2
1	na	sing	1:HIS88:NE2	2:FE21:FE
2	na	sing	1:HIS90:NE2	2:FE21:FE
3	na	sing	1:GLU94:OE1	2:FE21:FE
4	na	sing	1:HIS133:NE2	2:FE21:FE

Source organism

Exptl. method

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.9 %, Completeness: 63.6 %, Completeness (bb): 76.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	63.6 % (1414 of 2222)	70.2 % (816 of 1162)	51.6 % (444 of 861)	77.4 % (154 of 199)
Backbone	76.0 % (800 of 1052)	90.8 % (324 of 357)	62.0 % (327 of 527)	88.7 % (149 of 168)
Sidechain	56.3 % (754 of 1339)	60.5 % (487 of 805)	52.3 % (263 of 503)	12.9 % (4 of 31)
Aromatic	19.1 % (47 of 246)	35.0 % (43 of 123)	0.0 % (0 of 118)	80.0 % (4 of 5)
Methyl	95.0 % (152 of 160)	96.2 % (77 of 80)	93.8 % (75 of 80)

1. entity 1

MVQAWYMDDA PGDPRQPHRP DPGRPVGLEQ LRRLGVLYWK LDADKYENDP ELEKIRRERN YSWMDIITIC KDKLPNYEEK IKMFYEEHLH LDDEIRYILD GSGYFDVRDK EDQWIRIFME KGDMVTLPAG IYHRFTVDEK NYTKAMRLFV GEPVWTAYNR PADHFEARGQ YVKFLAQTA

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

Protein Blocks Logo

Calculated from 6 models in PDB: 7JXG, Strand ID: A Detail

Release date

2020-05-10

Citation

A Model for the Solution Structure of Human Fe(II)-Bound Acireductone Dioxygenase and Interactions with the Regulatory Domain of Matrix Metalloproteinase I (MMP-I)
Liu, X., Garber, A., Ryan, J., Deshpande, A., Ringe, D., Pochapsky, T.C.
Biochemistry (2020), 59, 4238-4249, PubMed 33135413 , DOI 10.1021/acs.biochem.0c00724 , Abstract

Related entities 1. acireductone dioxygenase, entity 1, : 1 : 3 : 95 entities Detail

Interaction partners 1. acireductone dioxygenase, entity 1, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

3 3D HNCA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

4 3D HN(CO)CA

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

6 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

8 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

9 3D 1H-15N TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	acireductone dioxygenase	[U-100% 13C; U-100% 15N]		500 uM
2	HEPES	natural abundance		50 mM
3	NaCl	natural abundance		100 mM

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr50269_3.str
Diamagnetism of the molecular assembly	False (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:88:HIS:NE2	2:1:FE2:FE	unknown	unknown	n/a
1:90:HIS:NE2	2:1:FE2:FE	unknown	unknown	n/a
1:94:GLU:OE1	2:1:FE2:FE	unknown	unknown	n/a
1:133:HIS:NE2	2:1:FE2:FE	unknown	unknown	n/a

Non-standard residues

None

Content subtype: bmr50269_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1567		92.7 (chain: 1, length: 179)
1	Chemical shift references	chem_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 179, Sequence coverage: 92.7%
- Total number of assignments
  - ¹H chemical shifts: 989
  - ¹³C chemical shifts: 425
  - ¹⁵N chemical shifts: 153
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: 1

Keywords dioxygenase, iron, methionine salvage