BMRBj - BMREntryMaster

Found 1 Document (0.411 seconds)

BMRB: 15100

2JNE

NMR structure of E.coli YfgJ protein modelled with two Zn+2 bound. Northeast Structural Genomics Consortium Target ER317.

Authors

Ramelot, T.A., Cort, J.R., Yee, A.A., Semesi, A., Johnathan, L., Arrowsmith, C.H., Kennedy, M.A.

Assembly

YfgJ with Zn+2

Entity

1. YfgJ protein (polymer, Thiol state: free and other bound), 101 monomers, 11468.09 Da Detail

FCLTLRRRYT MGSSHHHHHH SSGLVPRGSH MELHCPQCQH VLDQDNGHAR CRSCGEFIEM KALCPDCHQP LQVLKACGAV DYFCQHGHGL ISKKRVEFVL A

2. ZN (non-polymer), 65.409 × 2 Da

Total weight

11598.908 Da

Max. entity weight

11468.09 Da

Entity Connection

metal coordination 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	metal coordination	sing	1:CYS35:SG	2:ZN1:ZN

Source organism

Escherichia coli

Exptl. method

solution NMR

Data set

assigned_chemical_shifts, spectral_peak_list

Chem. Shift Complete

Sequence coverage: 76.2 %, Completeness: 72.2 %, Completeness (bb): 72.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	72.2 % (833 of 1154)	72.9 % (438 of 601)	71.0 % (319 of 449)	73.1 % (76 of 104)
Backbone	72.6 % (434 of 598)	72.8 % (150 of 206)	72.9 % (215 of 295)	71.1 % (69 of 97)
Sidechain	72.3 % (469 of 649)	72.9 % (288 of 395)	70.4 % (174 of 247)	100.0 % (7 of 7)
Aromatic	53.7 % (58 of 108)	59.3 % (32 of 54)	48.1 % (26 of 54)
Methyl	81.4 % (70 of 86)	81.4 % (35 of 43)	81.4 % (35 of 43)

1. YfgJ protein

FCLTLRRRYT MGSSHHHHHH SSGLVPRGSH MELHCPQCQH VLDQDNGHAR CRSCGEFIEM KALCPDCHQP LQVLKACGAV DYFCQHGHGL ISKKRVEFVL A

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 (±1) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Concentration
1	protein	[U-100% 13C]	1 (±0.2) mM
2	TRIS	natural abundance	10 (±1.0) mM
3	sodium chloride	natural abundance	250 (±5.0) mM
4	ZINC ION	natural abundance	10 (±1.0) uM
5	DTT	natural abundance	10 (±1.0) mM
6	sodium azide	natural abundance	0.01 (±0.001) %

LACS Plot; CA

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

Referencing offset: -0.27 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: -0.27 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.07 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.64 ppm, Outliers: 1 Detail

Release date

2007-10-02

Citation

NMR structure of E.coli YfgJ protein modelled with two Zn+2 bound. Northeast Structural Genomics Consortium Target ER317
Ramelot, T.A., Cort, J.R., Yee, A.A., Arrowsmith, C.H., Kennedy, M.A.

Related entities 1. YfgJ protein, : 1 : 4 entities Detail

Experiments performed 1 experiments Detail

Chemical shift validation 4 contents Detail

Properties

Input source #1: Assigned chemical shifts - Assigned chemical shifts	bmr15100_3.str
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	True (see coodinates for details)
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)

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
1:35:CYS:SG	2:1:ZN:ZN	reduced, CA 57.3, CB 31.9 ppm	unknown	n/a

Non-standard residues

None

Content subtype: bmr15100_3.str

#	Content subtype	Saveframe	Status	# of rows	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	851		70.3 (chain: 1, length: 101)
1	Chemical shift references	chemical_shift_reference_1	OK	3		No information

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: 1, Chain length: 101, Sequence coverage: 70.3%
- Total number of assignments
  - ¹H chemical shifts: 478
  - ¹³C chemical shifts: 302
  - ¹⁵N chemical shifts: 71
- Completeness of assignments
  - Entity_assemble_ID: 1
- Redox state of CYS
- 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: 1

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
37	GLN	CD	179.8
39	GLN	CD	180.4
44	GLN	CD	179.0
69	GLN	CD	180.0
72	GLN	CD	179.3
85	GLN	CD	180.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	601	410	68.2
¹³C chemical shifts	449	296	65.9
¹⁵N chemical shifts	111	71	64.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	206	139	67.5
¹³C chemical shifts	202	132	65.3
¹⁵N chemical shifts	97	64	66.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	395	271	68.6
¹³C chemical shifts	247	164	66.4
¹⁵N chemical shifts	14	7	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	46	34	73.9
¹³C chemical shifts	46	34	73.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	54	27	50.0
¹³C chemical shifts	54	26	48.1

Keywords all beta, C3H, C4, C4C3H zinc finger, Zn+2, C7H, two zinc, zinc fingers

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Found 1 Document (0.411 seconds)

BMRB: 15100

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. YfgJ protein, : 1 : 4 entities Detail

Experiments performed 1 experiments Detail

Instrument

Sample

Chemical shift validation 4 contents Detail