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- PDB-9i38: Solution structure of the de novo designed monoheme protein m4D2 ... -

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Basic information

Entry
Database: PDB / ID: 9i38
TitleSolution structure of the de novo designed monoheme protein m4D2 with bound iron(III) 2,4-dimethyldeuteroporphyrin IX
Componentsm4D2
KeywordsDE NOVO PROTEIN / Heme / cofactor binding / de novo designed / redox protein
Function / homologyFE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX
Function and homology information
Biological speciestest organism (others)
MethodSOLUTION NMR / simulated annealing
AuthorsWilliams, C. / Hutchins, G.H. / Molinaro, P.M. / Berrones-Reyes, J.C. / Lichtenstein, B.R. / Koder, R.L. / Anderson, J.L.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)B/W003449/1 United Kingdom
CitationJournal: To Be Published
Title: Solution structure of the de novo designed monoheme protein m4D2 with bound iron(III) 2,4-dimethyldeuteroporphyrin IX
Authors: Williams, C. / Hutchins, G.H. / Molinaro, P.M. / Berrones-Reyes, J.C. / Lichtenstein, B.R. / Koder, R.L. / Anderson, J.L.R.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: m4D2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,4852
Polymers12,8931
Non-polymers5921
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 20structures with the least restraint violations
RepresentativeModel #1closest to the average

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Components

#1: Protein m4D2


Mass: 12892.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: de novo designed / Source: (gene. exp.) test organism (others) / Plasmid: 151 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 express
#2: Chemical ChemComp-FDD / FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX


Mass: 592.466 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
112isotropic12D 1H-15N HSQC
122isotropic13D 1H-15N NOESY
2152isotropic12D 1H-15N HSQC
2162isotropic13D 1H-15N NOESY
332isotropic22D 1H-15N HSQC
342isotropic22D 1H-13C HSQC
352isotropic23D HN(CO)CA
372isotropic23D HNCA
3102isotropic23D HN(CA)CB
392isotropic23D HNCO
382isotropic23D 1H-13C NOESY
362isotropic23D H(CCO)NH
3142isotropic23D HN(CA)CO
3132isotropic23D (H)CCH-TOCSY
3122isotropic23D CBCA(CO)NH
3112isotropic23D 1H-15N NOESY
3182isotropic23D 1H-15N TOCSY
3172isotropic23D CC(CO)NH

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-15N] m4D2, 1 mM FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX, 20 mM potassium phosphate, 50 mM potassium chloride, 90% H2O/10% D2O15N Sample90% H2O/10% D2O
solution21 mM [U-100% 13C; U-100% 15N] m4D2, 1 mM FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX, 20 nM potassium phosphate, 50 mM potassium chloride, 90% H2O/10% D2O15N13C Sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMm4D2[U-15N]1
1 mMFE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IXnatural abundance1
20 mMpotassium phosphatenatural abundance1
50 mMpotassium chloridenatural abundance1
1 mMm4D2[U-100% 13C; U-100% 15N]2
1 mMFE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IXnatural abundance2
20 nMpotassium phosphatenatural abundance2
50 mMpotassium chloridenatural abundance2
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)Details
150 mM15N sample6.41 atm298 K
250 mM15N sample6.41 atm308 Khigher temp to resolve some peaks for assigment
350 mM15N13C sample6.41 atm308 Khigher temp to resolve some peaks for assigment
450 mM15N13C sample6.41 atm298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails
Bruker AVANCE III HDBrukerAVANCE III HD70011.7mm microcryoprobe
Bruker AVANCE III HDBrukerAVANCE III HD80025mm TCI cryoprobe

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Processing

NMR software
NameVersionDeveloperClassification
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure calculation
ARIA2.3.2Linge, O'Donoghue and Nilgesrefinement
CcpNmr Analysis2.4.2CCPNpeak picking
Refinement
MethodSoftware ordinalDetails
simulated annealing2CNS run through ARIA 2.3.2
simulated annealing3
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 20 / Conformers submitted total number: 20

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