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Found 1 Document (0.697 seconds)

BMRB: 15377

2JR7

Solution structure of human DESR1

Authors

Wu, F., Wu, J., Shi, Y.

Assembly

DESR1

Entity

1. DESR1 (polymer, Thiol state: all other bound), 89 monomers, 10186.04 Da Detail

MAVFHDEVEI EDFQYDEDSE TYFYPCPCGD NFSITKEDLE NGEDVATCPS CSLIIKVIYD KDQFVSGETV PAPSANKELV KLEHHHHHH

2. ZN (non-polymer), 65.409 Da

Total weight

10251.449 Da

Max. entity weight

10186.04 Da

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

torsion angle dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 92.1 %, Completeness: 84.6 %, Completeness (bb): 90.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	84.6 % (859 of 1015)	88.1 % (460 of 522)	80.0 % (323 of 404)	85.4 % (76 of 89)
Backbone	90.8 % (476 of 524)	90.9 % (160 of 176)	90.9 % (240 of 264)	90.5 % (76 of 84)
Sidechain	79.9 % (461 of 577)	86.7 % (300 of 346)	71.2 % (161 of 226)	0.0 % (0 of 5)
Aromatic	38.2 % (42 of 110)	67.3 % (37 of 55)	9.1 % (5 of 55)
Methyl	91.3 % (73 of 80)	97.5 % (39 of 40)	85.0 % (34 of 40)

1. DESR1

MAVFHDEVEI EDFQYDEDSE TYFYPCPCGD NFSITKEDLE NGEDVATCPS CSLIIKVIYD KDQFVSGETV PAPSANKELV KLEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 295 K, pH 7.0

#	Name	Isotope labeling	Concentration
1	entity_1	[U-99% 13C; U-99% 15N]	1.5 mM
2	TRIS	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	beta-mercaptoethanol	natural abundance	14 mM
5	H2O		90 %
6	D2O		10 %

Sample #2

Solvent system 99.99% D2O, Pressure 1 atm, Temperature 295 K, pH 7.0

#	Name	Isotope labeling	Concentration
7	entity_1	[U-99% 13C; U-99% 15N]	1.5 mM
8	TRIS	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	beta-mercaptoethanol	natural abundance	14 mM
11	D2O		99.9 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.799 ppm	internal	indirect	0.2514
¹H	water	protons	4.799 ppm	internal	direct	1.0
¹⁵N	water	protons	4.799 ppm	internal	indirect	0.1013

Referencing offset: -0.11 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.799 ppm	internal	indirect	0.2514
¹H	water	protons	4.799 ppm	internal	direct	1.0
¹⁵N	water	protons	4.799 ppm	internal	indirect	0.1013

Referencing offset: -0.11 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.799 ppm	internal	indirect	0.2514
¹H	water	protons	4.799 ppm	internal	direct	1.0
¹⁵N	water	protons	4.799 ppm	internal	indirect	0.1013

Referencing offset: 0.01 ppm, Outliers: 3 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	water	protons	4.799 ppm	internal	indirect	0.2514
¹H	water	protons	4.799 ppm	internal	direct	1.0
¹⁵N	water	protons	4.799 ppm	internal	indirect	0.1013

Referencing offset: 0.32 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2JR7, Strand ID: A Detail

Release date

2008-03-12

Citation

Solution structure of human DESR1, a CSL zinc-binding protein
Wu, F., Zhang, J., Sun, J., Huang, H., Ji, P., Chu, W., Yu, M., Yang, F., Wu, Z., Wu, J., Shi, Y.
Proteins (2008), 71, 514-518, PubMed 18214955 , DOI 10.1002/prot.21915 , Abstract

Related entities 1. DESR1, : 1 : 3 : 10 entities Detail

Interaction partners 1. DESR1, : 4 interactors Detail

More details for 4 interactors identified by 3 citations

Experiments performed 2 experiments Detail

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15377_2jr7.nef
Input source #2: Coordindates	2jr7.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	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)
1:26:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:28:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:48:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a
1:51:CYS:SG	2:1:ZN:ZN	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
B	1	ZN	ZINC ION	None

Sequence alignments

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

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

Chain assignments

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

Content subtype: combined_15377_2jr7.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	4		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	850		92.1 (chain: A, length: 89)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2143 (1)	noe	92.1 (chain: A, length: 89)
2	Distance restraints	CNS/XPLOR_distance_constraints_5	Warning	6 (1)	undefined	4.5 (chain: A, length: 89)
3	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	20 (1)	hbond	13.5 (chain: A, length: 89)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	60 (60)	.	48.3 (chain: A, length: 89)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 92.1%
- Total number of assignments
  - ¹H chemical shifts: 457
  - ¹³C chemical shifts: 317
  - ¹⁵N chemical shifts: 76
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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 (%)
¹H chemical shifts	522	457	87.5
¹³C chemical shifts	404	317	78.5
¹⁵N chemical shifts	89	76	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	176	160	90.9
¹³C chemical shifts	178	162	91.0
¹⁵N chemical shifts	84	76	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	346	297	85.8
¹³C chemical shifts	226	155	68.6
¹⁵N chemical shifts	5	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	39	95.1
¹³C chemical shifts	41	33	80.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	55	34	61.8
¹³C chemical shifts	55	0	0.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 92.1%
- Total number of restraints: 2133
- Weight of restraints: 1.0 (2133)
- Potential type of restraints: square-well-parabolic (2133)
- Range of distance target values: 2.4, 3.9 (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: CNS/XPLOR_distance_constraints_5
  - Status: Warning
  - Experiment type: undefined
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 4.5%
  - Total number of restraints: 6
  - Weight of restraints: 1.0 (6)
  - Potential type of restraints: square-well-parabolic (6)
  - Range of distance target values: 3.75, 3.75 (Å)
  - Distance restraints per residue
    - Chain_ID: A
    - Chain_ID: B
      None
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_3
    - Status: Warning
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 13.5%
    - Total number of restraints: 20
    - Weight of restraints: 1.0 (20)
    - Potential type of restraints: square-well-parabolic (20)
    - Range of distance target values: 2.05, 3.05 (Å)
    - Histogram of distance target values
    - Distance restraints per residue
      - Chain_ID: A
      - Chain_ID: B
        None
    - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 89, Sequence coverage: 48.3%
- Total number of restraints: 60
- Total number of restraints per polymer type: 60
- Weight of restraints: 1.0 (60)
- Potential type of restraints: square-well-parabolic (60)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue

Keywords CSL zinc finger, DESR1

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Found 1 Document (0.697 seconds)

BMRB: 15377

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. DESR1, : 1 : 3 : 10 entities Detail

Interaction partners 1. DESR1, : 4 interactors Detail

Experiments performed 2 experiments Detail

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail