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BMRB: 15352

2JS3

NMR Structure of protein Q6N9A4_RHOPA:Northeast Structural Genomics Consortium Target RpT8

Authors

SINGARAPU, K., WU, Y., YEE, A., ELETSKY, A., SUKUMARAN, D., GARCIA, M., XIAO, R., BANSAL, S., BARAN, M., GAETANO, M.T., JAMES, P.H., ARROWSMITH, C., SZYPERSKI, T.

Assembly

rpt8 dimer

Entity

1. rpt8 dimer (polymer, Thiol state: not present), 192 monomers, 20849.22 × 2 Da Detail

MGSSHHHHHH SSGRENLYFQ GMTDTAAEDV RKIATALLKT AIEIVSEEDG GAHNQCKLCG ASVPWLQTGD EIKHADDCPV VIAKQILSSR PKLHAVMGSS HHHHHHSSGR ENLYFQGMTD TAAEDVRKIA TALLKTAIEI VSEEDGGAHN QCKLCGASVP WLQTGDEIKH ADDCPVVIAK QILSSRPKLH AV

Total weight

41698.44 Da

Max. entity weight

20849.22 Da

Source organism

Rhodopseudomonas palustris

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 49.5 %, Completeness: 47.3 %, Completeness (bb): 47.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	47.3 % (998 of 2112)	47.6 % (517 of 1086)	46.5 % (384 of 826)	48.5 % (97 of 200)
Backbone	47.9 % (546 of 1140)	48.5 % (190 of 392)	47.2 % (265 of 562)	48.9 % (91 of 186)
Sidechain	46.7 % (537 of 1150)	47.1 % (327 of 694)	46.2 % (204 of 442)	42.9 % (6 of 14)
Aromatic	28.8 % (38 of 132)	31.8 % (21 of 66)	25.0 % (16 of 64)	50.0 % (1 of 2)
Methyl	52.8 % (112 of 212)	52.8 % (56 of 106)	52.8 % (56 of 106)

1. rpt8 dimer

Show sample condition

Sample #1

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-100% 13C; U-100% 15N]		0.5 mM

Sample #2

Pressure 1 atm, Temperature 298 K, pH 7.0

#	Name	Isotope labeling	Type	Concentration
2	entity	[U-50% 13C; U-50% 15N]		0.5 mM

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: -0.09 ppm, Outliers: 3 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: -0.09 ppm, Outliers: 3 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: 0.02 ppm, Outliers: 2 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: -0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JS3, Strand ID: A, B Detail

Release date

2007-08-28

Citation

NMR Structure of protein Q6N9A4_RHOPA
SINGARAPU, K., WU, Y., YEE, A., ELETSKY, A., SUKUMARAN, D., GARCIA, M., XIAO, R., BANSAL, S., BARAN, M., GAETANO, M., JAMES, P., ARROWSMITH, C., SZYPERSKI, T.

Related entities 1. rpt8 dimer, : 4 entities Detail

Experiments performed 7 experiments Detail

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15352_2js3.nef
Input source #2: Coordindates	2js3.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--------90------
MGSSHHHHHHSSGRENLYFQGMTDTAAEDVRKIATALLKTAIEIVSEEDGGAHNQCKLCGASVPWLQTGDEIKHADDCPVVIAKQILSSRPKLHAV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGMTDTAAEDVRKIATALLKTAIEIVSEEDGGAHNQCKLCGASVPWLQTGDEIKHADDCPVVIAKQILSSRPKLHAV

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

--------10--------20--------30--------40--------50--------60--------70--------80--------90------
MGSSHHHHHHSSGRENLYFQGMTDTAAEDVRKIATALLKTAIEIVSEEDGGAHNQCKLCGASVPWLQTGDEIKHADDCPVVIAKQILSSRPKLHAV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSSHHHHHHSSGRENLYFQGMTDTAAEDVRKIATALLKTAIEIVSEEDGGAHNQCKLCGASVPWLQTGDEIKHADDCPVVIAKQILSSRPKLHAV

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	96	0	0	100.0
B	B	96	0	0	100.0

Content subtype: combined_15352_2js3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	922		88.5 (chain: A, length: 96)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	OK	2410 (1)	noe	86.5 (chain: A, length: 96), 86.5 (chain: B, length: 96)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	Warning	638 (552)	.	87.5 (chain: A, length: 96), 87.5 (chain: B, length: 96)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 88.5%
- Total number of assignments
  - ¹³C chemical shifts: 357
  - ¹H chemical shifts: 478
  - ¹⁵N chemical shifts: 87
- Completeness of assignments
  - Entity_assemble_ID: A
- 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: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	413	357	86.4
¹H chemical shifts	543	478	88.0
¹⁵N chemical shifts	103	87	84.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	192	165	85.9
¹H chemical shifts	196	171	87.2
¹⁵N chemical shifts	93	81	87.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	221	192	86.9
¹H chemical shifts	347	307	88.5
¹⁵N chemical shifts	10	6	60.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	55	54	98.2
¹H chemical shifts	55	54	98.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	32	16	50.0
¹H chemical shifts	33	21	63.6
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 86.5%
  - Entity_assembly_ID: B, Chain length: 96, Sequence coverage: 86.5%
- Total number of restraints: 2407
- Weight of restraints: 1.0 (2407)
- Potential type of restraints: upper-bound-parabolic (2407)
- Range of distance target values: 2.59, 10.23 (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: Warning
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 96, Sequence coverage: 87.5%
  - Entity_assembly_ID: B, Chain length: 96, Sequence coverage: 87.5%
- Total number of restraints: 552
- Total number of restraints per polymer type: 552
- Weight of restraints: 1.0 (552)
- Potential type of restraints: square-well-parabolic (552)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
  - Chain_ID: B

Keywords homodimer, NMR spectroscopy, protein structure

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Found 1 Document (0.999 seconds)

BMRB: 15352

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. rpt8 dimer, : 4 entities Detail

Experiments performed 7 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

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NMR combined restraints 4 contents Detail