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- PDB-2hz8: QM/MM structure refined from NMR-structure of a single chain diir... -

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Basic information

Entry
Database: PDB / ID: 2hz8
TitleQM/MM structure refined from NMR-structure of a single chain diiron protein
ComponentsDe novo designed diiron protein
KeywordsDE NOVO PROTEIN / four-helix bundle
Function / homologyIL-4 antagonist (De novo design) like domain / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / 1. Step: Classical Molecular dynamics simulation starting from NMR-structure, using non-bonded model for metal-site. 2. step: QM, MM MD for relaxation of local frustrations at the metal site.
AuthorsCalhoun, J.R. / Liu, W. / Spiegel, K. / Dal Peraro, M. / Klein, M.L. / Wand, A.J. / DeGrado, W.F.
Citation
Journal: Structure / Year: 2008
Title: Solution NMR structure of a designed metalloprotein and complementary molecular dynamics refinement.
Authors: Calhoun, J.R. / Liu, W. / Spiegel, K. / Dal Peraro, M. / Klein, M.L. / Valentine, K.G. / Wand, A.J. / Degrado, W.F.
#1: Journal: J.Mol.Biol. / Year: 2003
Title: Computational design and characterization of a monomeric helical dinuclear metalloprotein.
Authors: Calhoun, J.R. / Kono, H. / Lahr, S. / Wang, W. / DeGrado, W.F. / Saven, J.G.
#2: Journal: Biopolymers / Year: 2005
Title: Artificial diiron proteins: from structure to function.
Authors: Calhoun, J.R. / Nastri, F. / Magloi, O. / Pavone, V. / Lombardi, A. / DeGrado, W.F.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999Sequence No suitable database references were found at time of processing

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: De novo designed diiron protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,6473
Polymers13,5161
Non-polymers1312
Water362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 1dynamical average of 300K trajectory
Representative

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Components

#1: Protein De novo designed diiron protein


Mass: 13516.417 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
1314D 13C/15N-separated NOESY
1414D 13C-separated NOESY
151HNHA
363IPAP-15N HSQC
NMR detailsText: The structure was first determined using triple-resonance spectrscopy. The structure was then further refined using classical MD followed by 5 ps of Car Parrinello hybrid QM/MM dynamics.

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Sample preparation

Details
Solution-IDContentsSolvent system
12 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O95% water, 5% D20
22 mM DUE FERRI SINGLE CHAIN U-15N, 10% 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O95% water, 5% D20
32 mM DUE FERRI SINGLE CHAIN U-15N, 13C, 2.5 mM Zn(II), 50 mM DUETERATED SODIUM ACETATE 10 mM NaCl, 5% D2O DIHEXANOYLPHOSPHATIDYLCHOLINE, DIMYRISTOYLPHOSPHATIDYLCHOLINE95% water, 5% D20
Sample conditionsIonic strength: 10 mM NaCl / pH: 6 / Pressure: ambient / Temperature: 308 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A. Brunger, P. Adams, M. Clore, P.Gros, M. Nilges, and R. Reedrefinement
NMRPipelinux9F. Delaglio, S. Grzesiek, A. Bax, Geerten, and W. Vuisterprocessing
Sparky3.11T.D. Goddard and D.G. Knellerdata analysis
VNMR6.1bP. Nicholas, D. Fushman, V. Ruchinsky, and D. Cowburncollection
NAMDversion 2.6Laxmikant, K, Skeel, R, Bhandarkar, M, Brunner, R, Gursoy, A, Krawetz, N, Phillips, J, Shinozaki, A, Varadarajan, K,Schulten, Krefinement
Amberversion 8Case, D. A., Cheatham, T. E., 3rd, Darden, T., Gohlke, H., Luo, R., Merz, K. M., Jr., Onufriev, A., Simmerling, C., Wang, B., Woods, R. J.refinement
QM/MM(Version 3.10), based on CPMD and GROMOSCPMD: Hutter, J, Alavi, A, Deutsch, T, Ballone, P, Bernasconi, M, Focher, P, Goedecker, S; GROMOS Scott WRP, Huhnenberger, PH, Tironi, TG, Mark, AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF: Laio, A., VandeVondele, J., Rothlisberger, U.refinement
RefinementMethod: 1. Step: Classical Molecular dynamics simulation starting from NMR-structure, using non-bonded model for metal-site. 2. step: QM, MM MD for relaxation of local frustrations at the metal site.
Software ordinal: 1
Details: Average over last ps of 5ps QM/MM trajectory. Two metal-site water molecules are included in the average. Other solvent molecules and counter ions are excluded. Atoms included in the QM-part ...Details: Average over last ps of 5ps QM/MM trajectory. Two metal-site water molecules are included in the average. Other solvent molecules and counter ions are excluded. Atoms included in the QM-part are indicated with a value of 1 in the beta-factor column, whereas atoms in the MM-part are indicated with a value of 0 in the beta-factor column.
NMR ensembleConformer selection criteria: dynamical average of 300K trajectory
Conformers calculated total number: 1 / Conformers submitted total number: 1

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