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PDB ID: 9i38
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_full
BMRB Entry DOI: doi:10.13018/BMR34977
MolProbity Validation Chart

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NMR-STAR v3 text file.
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Nicholas Rego and David Koes
3Dmol.js: molecular visualization with WebGL
Bioinformatics (2015) 31 (8): 1322-1324 doi:10.1093/bioinformatics/btu829

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Name: Solution structure of the de novo designed monoheme protein m4D2 with bound iron(III) 2,4-dimethyldeuteroporphyrin IX
Published: 2026-01-29

Title:

Solution structure of the de novo designed monoheme protein m4D2 with bound iron(III) 2,4-dimethyldeuteroporphyrin IX

Deposition date:

2025-01-22

Original release date:

2026-01-29

Authors:

Williams, C.; Hutchins, G.; Molinaro, P.; Berrones-Reyes, J.; Lichtenstein, B.; Koder, R.; Anderson, J.

Citation:

Citation: Williams, C.; Hutchins, G.; Molinaro, P.; Berrones-Reyes, J.; Lichtenstein, B.; Koder, R.; Anderson, J.. "Solution structure of the de novo designed monoheme protein m4D2 with bound iron(III) 2,4-dimethyldeuteroporphyrin IX" .

Assembly members:

Assembly members:
entity_1, polymer, 112 residues, 12892.566 Da.
entity_FDD, non-polymer, 592.466 Da.

Natural source:

Natural source: Common Name: not available Taxonomy ID: 457483 Superkingdom: not available Kingdom: not available Genus/species: test organism

Experimental source:

Experimental source: Production method: recombinant technology Host organism: Escherichia coli Vector: 151

Entity Sequences (FASTA):

Entity Sequences (FASTA):
entity_1: GSPELREKLRALIEQVYATG QEMLKNTSNSPELREKHRAL AEQVYATWQELLKNGSVSPS PELREKFRALLEQVYATGQE MLKNTSNSPELREKHRALAE QVIATWQELLKN

Data sets:

assigned_chemical_shifts
- assigned_chemical_shifts_1

Data type	Count
13C chemical shifts	457
15N chemical shifts	119
1H chemical shifts	778

Additional metadata:

Assembly
Samples and Experiments
Software
Spectrometers
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Assembly:

Entity Assembly ID	Entity Name	Entity ID
1	unit_1	1
2	unit_2	2

Entities:

Entity 1, unit_1 112 residues - 12892.566 Da.

1

GLY

SER

PRO

GLU

LEU

ARG

GLU

LYS

LEU

ARG

2

ALA

LEU

ILE

GLU

GLN

VAL

TYR

ALA

THR

GLY

3

GLN

GLU

MET

LEU

LYS

ASN

THR

SER

ASN

SER

4

PRO

GLU

LEU

ARG

GLU

LYS

HIS

ARG

ALA

LEU

5

ALA

GLU

GLN

VAL

TYR

ALA

THR

TRP

GLN

GLU

6

LEU

LYS

ASN

GLY

SER

VAL

SER

PRO

SER

7

PRO

GLU

LEU

ARG

GLU

LYS

PHE

ARG

ALA

LEU

8

LEU

GLU

GLN

VAL

TYR

ALA

THR

GLY

GLN

GLU

9

MET

LEU

LYS

ASN

THR

SER

ASN

SER

PRO

GLU

10

LEU

ARG

GLU

LYS

HIS

ARG

ALA

LEU

ALA

GLU

11

GLN

VAL

ILE

ALA

THR

TRP

GLN

GLU

LEU

12

LYS

ASN

Entity 2, unit_2 - C32 H32 Fe N4 O4 - 592.466 Da.

1

FDD

Samples:

sample_1: m4D2, [U-15N], 1 ± 0.2 mM; FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX 1 ± 0.2 mM; potassium phosphate 20 ± 5 mM; potassium chloride 50 ± 5 mM

sample_2: m4D2, [U-100% 13C; U-100% 15N], 1 ± 0.2 mM; FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX 1 ± 0.2 mM; potassium phosphate 20 ± 5 nM; potassium chloride 50 ± 5 mM

sample_conditions_1: ionic strength: 50 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

sample_conditions_2: ionic strength: 50 mM; pH: 6.4; pressure: 1 atm; temperature: 308 K

sample_conditions_3: ionic strength: 50 mM; pH: 6.4; pressure: 1 atm; temperature: 308 K

sample_conditions_4: ionic strength: 50 mM; pH: 6.4; pressure: 1 atm; temperature: 298 K

Experiments:

Name	Sample	Sample state	Sample conditions
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_1
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_1
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_3
2D 1H-13C HSQC	sample_2	isotropic	sample_conditions_3
3D HN(CO)CA	sample_2	isotropic	sample_conditions_3
3D H(CCO)NH	sample_2	isotropic	sample_conditions_3
3D HNCA	sample_2	isotropic	sample_conditions_3
3D 1H-13C NOESY	sample_2	isotropic	sample_conditions_3
3D HNCO	sample_2	isotropic	sample_conditions_3
3D HNCACB	sample_2	isotropic	sample_conditions_3
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_3
3D CBCA(CO)NH	sample_2	isotropic	sample_conditions_3
3D HCCH-TOCSY	sample_2	isotropic	sample_conditions_3
3D HNCACO	sample_2	isotropic	sample_conditions_3
2D 1H-15N HSQC	sample_2	isotropic	sample_conditions_2
3D 1H-15N NOESY	sample_2	isotropic	sample_conditions_2
3D CC(CO)NH	sample_2	isotropic	sample_conditions_3
3D 1H-15N TOCSY	sample_2	isotropic	sample_conditions_3

Software:

CcpNmr Analysis v2.4.2, CCPN - chemical shift assignment, peak picking

CNS v1.21, Brunger, Adams, Clore, Gros, Nilges and Read - structure calculation

ARIA v2.3.2, Linge, O'Donoghue and Nilges - refinement

NMR spectrometers:

Bruker AVANCE III HD 700 MHz
Bruker AVANCE III HD 800 MHz

Download HSQC peak lists in one of the following formats:
CSV: Backbone or all simulated peaks
SPARKY: Backbone or all simulated peaks

BMRB Entry 34977