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BMRB: 30245

5US5

Solution structure of the IreB homodimer

Authors

Lytle, B.L., Peterson, F.C., Volkman, B.F., Kristich, C.J.

Assembly

UPF0297 protein EF 1202

Entity

1. UPF0297 protein EF 1202 (polymer, Thiol state: not present), 89 monomers, 10544.69 × 2 Da Detail

MGFTDETVRF DFDDNRKKAI SETLETVYRA LEEKGYNPIN QIVGYLLSGD PAYIPRYQDA RNLIRRHERD EIMEELTKYY LANHGIDIK

Total weight

21089.38 Da

Max. entity weight

10544.69 Da

Source organism

Enterococcus faecalis V583

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.9 %, Completeness: 90.2 %, Completeness (bb): 96.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	90.2 % (967 of 1072)	89.0 % (500 of 562)	90.6 % (378 of 417)	95.7 % (89 of 93)
Backbone	96.2 % (508 of 528)	95.0 % (171 of 180)	97.3 % (255 of 262)	95.3 % (82 of 86)
Sidechain	85.0 % (534 of 628)	84.6 % (323 of 382)	85.4 % (204 of 239)	100.0 % (7 of 7)
Aromatic	59.6 % (56 of 94)	76.6 % (36 of 47)	42.6 % (20 of 47)
Methyl	96.7 % (89 of 92)	93.5 % (43 of 46)	100.0 % (46 of 46)

1. entity 1

MGFTDETVRF DFDDNRKKAI SETLETVYRA LEEKGYNPIN QIVGYLLSGD PAYIPRYQDA RNLIRRHERD EIMEELTKYY LANHGIDIK

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.6, Details 1.0 mM [U-98% 13C; U-98% 15N] IreB, 50 mM sodium phosphate, 350 mM sodium chloride, 0.02 mg/mL sodium azide, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
1	IreB	[U-98% 13C; U-98% 15N]	1.0 mM
2	sodium azide	natural abundance	0.02 mg/mL
3	sodium chloride	natural abundance	350 mM
4	sodium phosphate	natural abundance	50 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 318 K, pH 6.6, Details 0.5 mM [U-98% 13C; U-98% 15N] IreB, 50 mM sodium phosphate, 350 mM sodium chloride, 0.02 mg/mL sodium azid, 95% H2O/5% D2O.

#	Name	Isotope labeling	Concentration
5	IreB	[U-98% 13C; U-98% 15N]	0.5 mM
6	sodium azid	natural abundance	0.02 mg/mL
7	sodium chloride	natural abundance	350 mM
8	sodium phosphate	natural abundance	50 mM

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.68 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.68 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: 0.08 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	external	indirect	0.2514495
¹H	DSS	methyl protons	external	direct	1.0
¹⁵N	DSS	methyl protons	external	indirect	0.1013291

Referencing offset: -0.69 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 5US5, Strand ID: A, B Detail

Release date

2017-03-15

Citation

Structure and Dimerization of IreB, a Negative Regulator of Cephalosporin Resistance in Enterococcus faecalis
Hall, C.L., Lytle, B.L., Jensen, D.R., Hoff, J.S., Peterson, F.C., Volkman, B.F., Kristich, C.J.
J. Mol. Biol. (2017), 429, 2324-2336, PubMed 28551334 , DOI 10.1016/j.jmb.2017.05.019 , Abstract

Related entities 1. UPF0297 protein EF 1202, : 1 : 70 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_30245_5us5.nef
Input source #2: Coordindates	5us5.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80---------
MGFTDETVRFDFDDNRKKAISETLETVYRALEEKGYNPINQIVGYLLSGDPAYIPRYQDARNLIRRHERDEIMEELTKYYLANHGIDIK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGFTDETVRFDFDDNRKKAISETLETVYRALEEKGYNPINQIVGYLLSGDPAYIPRYQDARNLIRRHERDEIMEELTKYYLANHGIDIK

Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B

--------10--------20--------30--------40--------50--------60--------70--------80---------
MGFTDETVRFDFDDNRKKAISETLETVYRALEEKGYNPINQIVGYLLSGDPAYIPRYQDARNLIRRHERDEIMEELTKYYLANHGIDIK
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGFTDETVRFDFDDNRKKAISETLETVYRALEEKGYNPINQIVGYLLSGDPAYIPRYQDARNLIRRHERDEIMEELTKYYLANHGIDIK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	89	0	0	100.0
B	B	89	0	0	100.0

Content subtype: combined_30245_5us5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	1922		97.8 (chain: A, length: 89), 97.8 (chain: B, length: 89)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3264 (1)	noe	91.0 (chain: A, length: 89), 91.0 (chain: B, length: 89)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	214 (214)	.	75.3 (chain: A, length: 89), 75.3 (chain: B, length: 89)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 97.8%
  - Entity_assembly_ID: B, Chain length: 89, Sequence coverage: 97.8%
- Total number of assignments
  - ¹H chemical shifts: 996
  - ¹³C chemical shifts: 750
  - ¹⁵N chemical shifts: 176
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
21	SER	HG	6.227

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	562	497	88.4
¹³C chemical shifts	417	375	89.9
¹⁵N chemical shifts	101	88	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	173	96.1
¹³C chemical shifts	178	171	96.1
¹⁵N chemical shifts	86	81	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	382	324	84.8
¹³C chemical shifts	239	204	85.4
¹⁵N chemical shifts	15	7	46.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	46	95.8
¹³C chemical shifts	48	47	97.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	36	76.6
¹³C chemical shifts	47	20	42.6

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
21	SER	HG	6.227

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	562	497	88.4
¹³C chemical shifts	417	375	89.9
¹⁵N chemical shifts	101	88	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	180	173	96.1
¹³C chemical shifts	178	171	96.1
¹⁵N chemical shifts	86	81	94.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	382	324	84.8
¹³C chemical shifts	239	204	85.4
¹⁵N chemical shifts	15	7	46.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	48	46	95.8
¹³C chemical shifts	48	47	97.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	47	36	76.6
¹³C chemical shifts	47	20	42.6

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 91.0%
  - Entity_assembly_ID: B, Chain length: 89, Sequence coverage: 91.0%
- Total number of restraints: 3264
- Weight of restraints: 1.0 (3264)
- Potential type of restraints: upper-bound-parabolic (3264)
- Range of distance target values: 2.35, 6.22 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 75.3%
  - Entity_assembly_ID: B, Chain length: 89, Sequence coverage: 75.3%
- Total number of restraints: 214
- Total number of restraints per polymer type: 214
- Weight of restraints: 1.0 (214)
- Potential type of restraints: square-well-parabolic (214)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords CESG, Center for Eukaryotic Structural Genomics, IreB, PSI-2, Protein Structure Initiative, Structural Genomics, Structure from MOLMOL, dimer

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Found 1 Document (0.875 seconds)

BMRB: 30245

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. UPF0297 protein EF 1202, : 1 : 70 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail