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BMRB: 17421

2L8R

Solution structure of human protein C6orf130 in complex with ADP-ribose

Authors

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

Assembly

C6orf130

Entity

1. C6orf130 (polymer, Thiol state: all free), 151 monomers, 16879.29 Da Detail

GSSLNEDPEG SRITYVKGDL FACPKTDSLA HCISEDCRMG AGIAVLFKKK FGGVQELLNQ QKKSGEVAVL KRDGRYIYYL ITKKRASHKP TYENLQKSLE AMKSHCLKNG VTDLSMPRIG CGLDRLQWEN VSAMIEEVFE ATDIKITVYT L

2. APR (non-polymer, Thiol state: not present), 559.316 Da

Total weight

17438.605 Da

Max. entity weight

16879.29 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT., torsion angle dynamics, AUTOMATED METHODS WERE USED FOR BACKBONE CHEMICAL SHIFT ASSIGNMENT AND ITERATIVE NOE REFINEMENT. FINAL STRUCTURES WERE OBTAINED BY MOLECULAR DYNAMICS IN EXPLICIT SOLVENT

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 94.8 %, Completeness (bb): 99.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.8 % (1672 of 1764)	93.4 % (860 of 921)	95.5 % (654 of 685)	100.0 % (158 of 158)
Backbone	99.2 % (891 of 898)	98.4 % (305 of 310)	99.5 % (439 of 441)	100.0 % (147 of 147)
Sidechain	91.4 % (919 of 1005)	90.8 % (555 of 611)	92.2 % (353 of 383)	100.0 % (11 of 11)
Aromatic	82.1 % (92 of 112)	100.0 % (56 of 56)	63.6 % (35 of 55)	100.0 % (1 of 1)
Methyl	98.8 % (164 of 166)	98.8 % (82 of 83)	98.8 % (82 of 83)

1. C6orf130

GSSLNEDPEG SRITYVKGDL FACPKTDSLA HCISEDCRMG AGIAVLFKKK FGGVQELLNQ QKKSGEVAVL KRDGRYIYYL ITKKRASHKP TYENLQKSLE AMKSHCLKNG VTDLSMPRIG CGLDRLQWEN VSAMIEEVFE ATDIKITVYT L

Show sample condition

Sample

Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.75 mM C6orf130 U-15N/13C, 1.875 mM ADP-ribose, 20 mM BisTris, 200 mM sodium chloride, 2 mM DTT

#	Name	Isotope labeling	Concentration
1	C6orf130	[U-100% 13C; U-100% 15N]	0.75 mM
2	ADP-ribose	natural abundance	1.875 mM
3	BisTris	natural abundance	20 mM
4	NaCl	natural abundance	200 mM
5	DTT	natural abundance	2 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

Protein Blocks Logo

Calculated from 20 models in PDB: 2L8R, Strand ID: A Detail

Release date

2011-03-07

Related entities 1. C6orf130, : 1 : 7 : 22 entities Detail

Interaction partners 1. C6orf130, : 2 interactors Detail

More details for 2 interactors identified by 1 citations

Experiments performed 4 experiments Detail

1 3D_15N-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

State isotropic, Solvent system 93% H2O, 7% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.75 mM C6orf130 U-15N/13C, 1.875 mM ADP-ribose, 20 mM BisTris, 200 mM sodium chloride, 2 mM DTT

#	Name	Isotope labeling	Concentration
1	C6orf130	[U-100% 13C; U-100% 15N]	0.75 mM
2	ADP-ribose	natural abundance	1.875 mM
3	BisTris	natural abundance	20 mM
4	NaCl	natural abundance	200 mM
5	DTT	natural abundance	2 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

2 3D_13C-separated_NOESY

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	C6orf130	[U-100% 13C; U-100% 15N]	0.75 mM
2	ADP-ribose	natural abundance	1.875 mM
3	BisTris	natural abundance	20 mM
4	NaCl	natural abundance	200 mM
5	DTT	natural abundance	2 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

3 3D_13C-separated_NOESY (AROMATIC)

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	C6orf130	[U-100% 13C; U-100% 15N]	0.75 mM
2	ADP-ribose	natural abundance	1.875 mM
3	BisTris	natural abundance	20 mM
4	NaCl	natural abundance	200 mM
5	DTT	natural abundance	2 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

4 3D F1-13C-flitered/F3-13C-edited 1H-13C NOESY aliphatic

Instrument

Bruker Avance II - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
1	C6orf130	[U-100% 13C; U-100% 15N]	0.75 mM
2	ADP-ribose	natural abundance	1.875 mM
3	BisTris	natural abundance	20 mM
4	NaCl	natural abundance	200 mM
5	DTT	natural abundance	2 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17421_2l8r.nef
Input source #2: Coordindates	2l8r.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

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	APR	ADENOSINE-5-DIPHOSPHORIBOSE	Assigned chemical shifts

Sequence alignments

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

-------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-
GSSLNEDPEGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLE
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSSLNEDPEGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLE
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

------110-------120-------130-------140-------150--
AMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL
|||||||||||||||||||||||||||||||||||||||||||||||||||
AMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL
-------110-------120-------130-------140-------150-

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	151	0	0	100.0

Content subtype: combined_17421_2l8r.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1684		99.3 (chain: A, length: 151), 100.0 (chain: B, length: 1)
1	Distance restraints	DYANA/DIANA_distance_constraints_3	Warning	2815 (1)	noe	96.7 (chain: A, length: 151)
2	Distance restraints	DYANA/DIANA_distance_constraints_5	Warning	2815 (1)	noe	96.7 (chain: A, length: 151)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	211 (211)	.	86.8 (chain: A, length: 151)
2	Dihedral angle restraints	DYANA/DIANA_dihedral_4	OK	211 (211)	.	86.8 (chain: A, length: 151)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1

Status: Warning

Sequence coverage of experimental data

Entity_assembly_ID: A, Chain length: 151, Sequence coverage: 99.3%

-------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-
GSSLNEDPEGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLE
 |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
.SSLNEDPEGSRITYVKGDLFACPKTDSLAHCISEDCRMGAGIAVLFKKKFGGVQELLNQQKKSGEVAVLKRDGRYIYYLITKKRASHKPTYENLQKSLE

------110-------120-------130-------140-------150--
AMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL
|||||||||||||||||||||||||||||||||||||||||||||||||||
AMKSHCLKNGVTDLSMPRIGCGLDRLQWENVSAMIEEVFEATDIKITVYTL

Entity_assembly_ID: B, Chain length: 1, Sequence coverage: 100.0%

-
X
|
X

Total number of assignments
- ¹H chemical shifts: 874
- ¹³C chemical shifts: 649
- ¹⁵N chemical shifts: 161

Completeness of assignments

Entity_assemble_ID: A

Excluded Atom_ID in statistics

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
29	SER	HG	6.358
32	HIS	HD1	8.42
32	HIS	ND1	163.811
33	CYS	HG	1.475
35	SER	HG	5.729
38	CYS	HG	1.763
79	TYR	HH	11.321
80	TYR	HH	9.993
83	THR	HG1	5.069
92	THR	HG1	5.344
107	CYS	HG	2.236
122	CYS	HG	3.416
143	THR	HG1	5.463

All atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	921	850	92.3
¹³C chemical shifts	685	649	94.7
¹⁵N chemical shifts	165	160	97.0

Backbone atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	310	305	98.4
¹³C chemical shifts	302	297	98.3
¹⁵N chemical shifts	147	145	98.6

Side chain atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	611	545	89.2
¹³C chemical shifts	383	352	91.9
¹⁵N chemical shifts	18	15	83.3

Methyl group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	87	85	97.7
¹³C chemical shifts	87	85	97.7

Aromatic group atoms

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	56	56	100.0
¹³C chemical shifts	55	35	63.6
¹⁵N chemical shifts	1	1	100.0

Entity_assemble_ID: B

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

Comp_index_ID	Comp_ID
1	APR

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_3
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 151, Sequence coverage: 96.7%
- Total number of restraints: 2815
- Weight of restraints: 1.0 (2815)
- Potential type of restraints: upper-bound-parabolic (2815)
- Range of distance target values: 2.25, 5.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
  - Chain_ID: B
    None
- Distance restraints on contact map
- Saveframe: DYANA/DIANA_distance_constraints_5
  - Status: Warning
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 151, Sequence coverage: 96.7%
  - Total number of restraints: 2815
  - Weight of restraints: 1.0 (2815)
  - Potential type of restraints: upper-bound-parabolic (2815)
  - Range of distance target values: 2.25, 5.5 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 151, Sequence coverage: 86.8%
- Total number of restraints: 211
- Total number of restraints per polymer type: 211
- Weight of restraints: 1.0 (211)
- Potential type of restraints: square-well-parabolic (211)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A
- Saveframe: DYANA/DIANA_dihedral_4
  - Status: OK
  - Experiment type: .
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 151, Sequence coverage: 86.8%
  - Total number of restraints: 211
  - Total number of restraints per polymer type: 211
  - Weight of restraints: 1.0 (211)
  - Potential type of restraints: square-well-parabolic (211)
  - Plot of Phi-Psi angle restraints
  - Dihedral angle restraints per residue
    - Chain_ID: A

Keywords adenosine-5-diphosphoribose, BC011709, C6orf130, Center for Eukaryotic Structural Genomics, macro domain, Protein Structure Initiative, PSI, Structural Genomics

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Found 1 Document (0.994 seconds)

BMRB: 17421

Sample

Related entities 1. C6orf130, : 1 : 7 : 22 entities Detail

Interaction partners 1. C6orf130, : 2 interactors Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail