BMRB Entry 15301
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full
BMRB Entry DOI: doi:10.13018/BMR15301
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Title: Solution model of crosslinked complex of cytochrome c and adrenodoxin PubMed: 18439013
Deposition date: 2007-06-12 Original release date: 2008-06-12
Authors: Xu, Xingfu; Reinle, Wolfgang; Hannemann, Frank; Konarev, Peter; Svergun, Dmitri; Bernhardt, Rita; Ubbink, Marcellus
Citation: Xu, Xingfu; Reinle, Wolfgang; Hannemann, Frank; Konarev, Peter; Svergun, Dmitri; Bernhardt, Rita; Ubbink, Marcellus. "Dynamics in a pure encounter complex of two proteins studied by solution scattering and paramagnetic NMR spectroscopy" J. Am. Chem. Soc. 130, 6395-6403 (2008).
Assembly members:
Cytc, polymer, 108 residues, Formula weight is not available
Adx, polymer, 105 residues, Formula weight is not available
HEME C, non-polymer, 618.503 Da.
FE2/S2 (INORGANIC) CLUSTER, non-polymer, 175.820 Da.
Natural source: Common Name: baker Taxonomy ID: 4932 Superkingdom: not available Kingdom: not available Genus/species: Eukaryota Fungi
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
Cytc: TEFKAGSAKKGATLFKTRCL
QCHTVEKGGPHKCGPNLHGI
FGRHSGQAEGYSYTDANIKK
NVLWDENNMSEYLTNPKKYI
PGTKMAFGGLKKEKDRNDLI
TYLKKATE
Adx: EDKITVHFINRDGETLTTKG
KIGDSLLDVVVQNNLDIDGF
GACEGTLACSTCHLIFEQHI
FEKLEAITDEENDMLDCAYG
LTDRSRLGCQISLTKAMDNM
TVRVP
- assigned_chemical_shifts
| Data type | Count |
| 15N chemical shifts | 146 |
| 1H chemical shifts | 146 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | CcV28C | 1 |
| 2 | AdxL80C | 2 |
| 3 | HEME C | 3 |
| 4 | FE2/S2 (INORGANIC) CLUSTER | 4 |
Entities:
Entity 1, CcV28C 108 residues - Formula weight is not available
Residues -4-0 represent a non-native tag
| 1 | THR | GLU | PHE | LYS | ALA | GLY | SER | ALA | LYS | LYS | ||||
| 2 | GLY | ALA | THR | LEU | PHE | LYS | THR | ARG | CYS | LEU | ||||
| 3 | GLN | CYS | HIS | THR | VAL | GLU | LYS | GLY | GLY | PRO | ||||
| 4 | HIS | LYS | CYS | GLY | PRO | ASN | LEU | HIS | GLY | ILE | ||||
| 5 | PHE | GLY | ARG | HIS | SER | GLY | GLN | ALA | GLU | GLY | ||||
| 6 | TYR | SER | TYR | THR | ASP | ALA | ASN | ILE | LYS | LYS | ||||
| 7 | ASN | VAL | LEU | TRP | ASP | GLU | ASN | ASN | MET | SER | ||||
| 8 | GLU | TYR | LEU | THR | ASN | PRO | LYS | LYS | TYR | ILE | ||||
| 9 | PRO | GLY | THR | LYS | MET | ALA | PHE | GLY | GLY | LEU | ||||
| 10 | LYS | LYS | GLU | LYS | ASP | ARG | ASN | ASP | LEU | ILE | ||||
| 11 | THR | TYR | LEU | LYS | LYS | ALA | THR | GLU |
Entity 2, AdxL80C 105 residues - Formula weight is not available
The first two residues have no coordinates in AYF
| 1 | GLU | ASP | LYS | ILE | THR | VAL | HIS | PHE | ILE | ASN | ||||
| 2 | ARG | ASP | GLY | GLU | THR | LEU | THR | THR | LYS | GLY | ||||
| 3 | LYS | ILE | GLY | ASP | SER | LEU | LEU | ASP | VAL | VAL | ||||
| 4 | VAL | GLN | ASN | ASN | LEU | ASP | ILE | ASP | GLY | PHE | ||||
| 5 | GLY | ALA | CYS | GLU | GLY | THR | LEU | ALA | CYS | SER | ||||
| 6 | THR | CYS | HIS | LEU | ILE | PHE | GLU | GLN | HIS | ILE | ||||
| 7 | PHE | GLU | LYS | LEU | GLU | ALA | ILE | THR | ASP | GLU | ||||
| 8 | GLU | ASN | ASP | MET | LEU | ASP | CYS | ALA | TYR | GLY | ||||
| 9 | LEU | THR | ASP | ARG | SER | ARG | LEU | GLY | CYS | GLN | ||||
| 10 | ILE | SER | LEU | THR | LYS | ALA | MET | ASP | ASN | MET | ||||
| 11 | THR | VAL | ARG | VAL | PRO |
Entity 3, HEME C - C34 H34 Fe N4 O4 - 618.503 Da.
| 1 | HEC |
Entity 4, FE2/S2 (INORGANIC) CLUSTER - Fe2 S2 - 175.820 Da.
| 1 | FES |
Samples:
CcV28C_AdxL80C: CcV28C, [U-98% 15N], 0.2 – 0.6 mM; AdxL80C0.2 – 0.6 mM; potassium phosphate 20 mM
AdxL80C_CcV28C: AdxL80C, [U-98% 15N], 0.2 – 0.6 mM; CcV28C0.2 – 0.6 mM; potassium phosphate 20 mM
CcV28C: CcV28C, [U-98% 15N], 1.0 mM; DTT 5 mM; potassium phosphate 20 mM
AdxL80C: AdxL80C, [U-98% 15N], 0.5 – 0.8 mM; DTT 5 mM; potassium phosphate 20 mM
sample_conditions_1: pH: 7.4; pressure: 1 atm; temperature: 285 K
sample_conditions_2: ionic strength: 0.4 M; pH: 7.4; pressure: 1 atm; temperature: 301 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | CcV28C_AdxL80C | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | AdxL80C_CcV28C | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | CcV28C_AdxL80C | isotropic | sample_conditions_2 |
| 3D 1H-15N NOESY | AdxL80C_CcV28C | isotropic | sample_conditions_2 |
| 2D 1H-15N HSQC | CcV28C | isotropic | sample_conditions_1 |
| 2D 1H-15N HSQC | AdxL80C | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | AdxL80C | isotropic | sample_conditions_1 |
| 3D 1H-15N TOCSY | AdxL80C | isotropic | sample_conditions_1 |
Software:
AZARA, Boucher - processing
ANSIG, Kraulis - data analysis
X-PLOR NIH, Schwieters, Kuszewski, Tjandra and Clore - refinement
NMR spectrometers:
- Bruker DMX 600 MHz
Related Database Links:
| PDB | |
| BMRB | 131 17845 17846 17903 17904 19638 4566 7390 |
| DBJ | GAA24396 BAA00362 BAA00363 |
| EMBL | CAA24605 CAA89576 CAY80764 |
| GB | AAA62856 AAA88751 AAB59344 AHY79034 AJP39735 AAA30357 AAA30358 AAB21264 AAI09850 ABQ13041 |
| PRF | 1409323A |
| REF | NP_012582 NP_851354 XP_005889885 XP_010861227 |
| SP | P00044 P00257 |
| TPG | DAA08835 DAA22428 |
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts