BMRB Entry 16428
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PDB ID:
Entry in NMR Restraints Grid
Validation report in NRG-CING
Chem Shift validation: AVS_anomalous, AVS_full, LACS, SPARTA
BMRB Entry DOI: doi:10.13018/BMR16428
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Title: The structure of the KlcA and ArdB proteins show a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro. PubMed: 20007596
Deposition date: 2009-07-28 Original release date: 2010-02-02
Authors: Serfiotis-Mitsa, Dimitra; Herbert, Andrew; Roberts, Gareth; Soares, Dinesh; White, John; Blakely, Garry; Uhrin, Dusan; Dryden, David
Citation: Serfiotis-Mitsa, Dimitra; Herbert, Andrew; Roberts, Gareth; Soares, Dinesh; White, John; Blakely, Garry; Uhrin, Dusan; Dryden, David. "The structure of the KlcA and ArdB proteins reveals a novel fold and antirestriction activity against Type I DNA restriction systems in vivo but not in vitro." Nucleic Acids Res. 38, 1723-1737 (2010).
Assembly members:
KlcA and ArdB proteins, polymer, 142 residues, Formula weight is not available
Natural source: Common Name: B. pertussis Taxonomy ID: 520 Superkingdom: Bacteria Kingdom: not available Genus/species: Bordetella pertussis
Experimental source: Production method: recombinant technology Host organism: Escherichia coli
Entity Sequences (FASTA):
KlcA and ArdB proteins: MNTEEQPVTASLVAEAQRLD
FLPTYFGPRLMMRGEALVYA
WMRRLCERYNGAYWHYYALS
DGGFYMAPDLAGRLEIEVNG
NGFRGELSADAAGIVATLFA
LGQLAAEIADTDAADALIDR
YHFLRGFAAGHPEAAAIYRA
ID
- assigned_chemical_shifts
- RDCs
| Data type | Count |
| 13C chemical shifts | 559 |
| 15N chemical shifts | 149 |
| 1H chemical shifts | 897 |
| residual dipolar couplings | 110 |
Additional metadata:
Assembly:
| Entity Assembly ID | Entity Name | Entity ID |
|---|---|---|
| 1 | KlcA and ArdB proteins | 1 |
Entities:
Entity 1, KlcA and ArdB proteins 142 residues - Formula weight is not available
| 1 | MET | ASN | THR | GLU | GLU | GLN | PRO | VAL | THR | ALA | ||||
| 2 | SER | LEU | VAL | ALA | GLU | ALA | GLN | ARG | LEU | ASP | ||||
| 3 | PHE | LEU | PRO | THR | TYR | PHE | GLY | PRO | ARG | LEU | ||||
| 4 | MET | MET | ARG | GLY | GLU | ALA | LEU | VAL | TYR | ALA | ||||
| 5 | TRP | MET | ARG | ARG | LEU | CYS | GLU | ARG | TYR | ASN | ||||
| 6 | GLY | ALA | TYR | TRP | HIS | TYR | TYR | ALA | LEU | SER | ||||
| 7 | ASP | GLY | GLY | PHE | TYR | MET | ALA | PRO | ASP | LEU | ||||
| 8 | ALA | GLY | ARG | LEU | GLU | ILE | GLU | VAL | ASN | GLY | ||||
| 9 | ASN | GLY | PHE | ARG | GLY | GLU | LEU | SER | ALA | ASP | ||||
| 10 | ALA | ALA | GLY | ILE | VAL | ALA | THR | LEU | PHE | ALA | ||||
| 11 | LEU | GLY | GLN | LEU | ALA | ALA | GLU | ILE | ALA | ASP | ||||
| 12 | THR | ASP | ALA | ALA | ASP | ALA | LEU | ILE | ASP | ARG | ||||
| 13 | TYR | HIS | PHE | LEU | ARG | GLY | PHE | ALA | ALA | GLY | ||||
| 14 | HIS | PRO | GLU | ALA | ALA | ALA | ILE | TYR | ARG | ALA | ||||
| 15 | ILE | ASP |
Samples:
sample_1: KlcA, [U-98% 13C; U-98% 15N], 0.7 mM; sodium acetate, [U-100% 2H], 20 mM; sodium azide 0.05%; H2O 90%; D2O 10%
sample_2: KlcA, [U-98% 15N], 0.7 mM; sodium acetate, [U-100% 2H], 20 mM; sodium azide 0.05%; Pf1 phage 6.25 mg; H2O 90%; D2O 10%
sample_3: KlcA, [U-98% 15N], 0.7 mM; sodium acetate, [U-100% 2H], 20 mM; sodium azide 0.05%; H2O 90%; D2O 10%
sample_conditions_1: ionic strength: 20 mM; pH: 6.0; pressure: 1 atm; temperature: 298 K
Experiments:
| Name | Sample | Sample state | Sample conditions |
|---|---|---|---|
| 2D 1H-15N HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D CBCANH | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCO | sample_1 | isotropic | sample_conditions_1 |
| 3D HNCACO | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHANH | sample_1 | isotropic | sample_conditions_1 |
| 3D HBHA(CO)NH | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC (Aromatic Selective) | sample_1 | isotropic | sample_conditions_1 |
| 3D H(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D C(CCO)NH | sample_1 | isotropic | sample_conditions_1 |
| 3D HCCH-TOCSY | sample_1 | isotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-15N NOESY | sample_1 | isotropic | sample_conditions_1 |
| 3D 1H-13C NOESY | sample_1 | isotropic | sample_conditions_1 |
| 2D HBCBCGCDHD | sample_1 | isotropic | sample_conditions_1 |
| 2D HBCBCGCDCEHE | sample_1 | isotropic | sample_conditions_1 |
| T1 | sample_3 | isotropic | sample_conditions_1 |
| T2 | sample_3 | isotropic | sample_conditions_1 |
| Heteronuclear NOE | sample_3 | isotropic | sample_conditions_1 |
| IPAP for RDC measurement | sample_2 | anisotropic | sample_conditions_1 |
| 2D 1H-13C HSQC | sample_1 | isotropic | sample_conditions_1 |
Software:
TOPSPIN v1.3, Bruker Biospin - collection
CYANA v2.1, Guntert, Mumenthaler and Wuthrich - structure solution
CNS v1.1, Brunger, Adams, Clore, Gros, Nilges and Read - refinement
ANALYSIS v1.0.15, CCPN - chemical shift assignment, data analysis, peak picking
AZARA v2.7, Boucher - processing
ProcheckNMR v3.5, Laskowski and MacArthur - Structure Validation
WhatIF, Vriend - Structure Validation
TALOS, Cornilescu, Delaglio and Bax - data analysis
NMR spectrometers:
- Bruker Avance 800 MHz
- Bruker Avance 600 MHz
Download simulated HSQC data in one of the following formats:
CSV: Backbone
or all simulated shifts
SPARKY: Backbone
or all simulated shifts