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Found 1 Document (1.386 seconds)

BMRB: 18095

2LM1

Solution NMR Structure of Lysine-specific demethylase lid from Drosophila melanogaster, Northeast Structural Genomics Consortium Target FR824D

Authors

Mills, J.L., Lee, D., Kohan, E., Sahdev, S., Acton, T.B., Xiao, R., Everett, J.K., Montelione, G.T., Szyperski, T.

Assembly

FR824D

Entity

1. FR824D (polymer, Thiol state: not present), 107 monomers, 12471.32 Da Detail

PRVQRLNELE AKTRVKLNFL DQIAKFWELQ GSSLKIPMVE RKALDLYTLH RIVQEEGGME QTTKDRKWAK VANRMQYPSS KSVGATLKAH YERILHPFEV YTSGKVL

Formula weight

12471.32 Da

Source organism

Drosophila melanogaster

Exptl. method

solution NMR

Refine. method

torsion angle dynamics, molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 99.1 %, Completeness: 91.5 %, Completeness (bb): 97.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.5 % (1209 of 1321)	90.9 % (633 of 696)	90.6 % (463 of 511)	99.1 % (113 of 114)
Backbone	97.2 % (616 of 634)	97.2 % (209 of 215)	96.5 % (305 of 316)	99.0 % (102 of 103)
Sidechain	87.8 % (693 of 789)	88.1 % (424 of 481)	86.9 % (258 of 297)	100.0 % (11 of 11)
Aromatic	65.3 % (64 of 98)	77.6 % (38 of 49)	51.1 % (24 of 47)	100.0 % (2 of 2)
Methyl	91.8 % (112 of 122)	93.4 % (57 of 61)	90.2 % (55 of 61)

1. FR824D

PRVQRLNELE AKTRVKLNFL DQIAKFWELQ GSSLKIPMVE RKALDLYTLH RIVQEEGGME QTTKDRKWAK VANRMQYPSS KSVGATLKAH YERILHPFEV YTSGKVL

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.3 mM [U-5% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	FR824D	[U-5% 13C; U-100% 15N]	1.3 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	5 mM
9	sodium azide	natural abundance	0.02 %
10	TRIS	natural abundance	10 mM

LACS Plot; CA

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

Referencing offset: -0.18 ppm, Outliers: 3 Detail

LACS Plot; CB

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

Referencing offset: -0.18 ppm, Outliers: 3 Detail

LACS Plot; HA

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

Referencing offset: 0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

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

Referencing offset: 0.01 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LM1, Strand ID: A Detail

Release date

2011-11-30

Related entities 1. FR824D, : 1 : 2 : 106 entities Detail

Interaction partners 1. FR824D, : 8 interactors Detail

More details for 8 interactors identified by 4 citations

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

2 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

5 3D HCCH-COSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

6 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Varian INOVA - 750 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

7 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.3 mM [U-5% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
6	FR824D	[U-5% 13C; U-100% 15N]	1.3 mM
7	sodium chloride	natural abundance	100 mM
8	DTT	natural abundance	5 mM
9	sodium azide	natural abundance	0.02 %
10	TRIS	natural abundance	10 mM

8 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

9 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.2 mM [U-100% 13C; U-100% 15N] FR824D, 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	FR824D	[U-100% 13C; U-100% 15N]	1.1 mM
2	sodium chloride	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	sodium azide	natural abundance	0.02 %
5	TRIS	natural abundance	10 mM

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18095_2lm1.nef
Input source #2: Coordindates	2lm1.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

----220-------230-------240-------250-------260-------270-------280-------290-------300-------310---
PRVQRLNELEAKTRVKLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKDRKWAKVANRMQYPSSKSVGATLKAHYERILHPFEV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PRVQRLNELEAKTRVKLNFLDQIAKFWELQGSSLKIPMVERKALDLYTLHRIVQEEGGMEQTTKDRKWAKVANRMQYPSSKSVGATLKAHYERILHPFEV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

----320
YTSGKVL
|||||||
YTSGKVL
-------

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	107	0	0	100.0

Content subtype: combined_18095_2lm1.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1212		99.1 (chain: A, length: 107)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2475 (1)	noe	98.1 (chain: A, length: 107)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	94 (94)	.	60.7 (chain: A, length: 107)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 99.1%
- Total number of assignments
  - ¹H chemical shifts: 636
  - ¹³C chemical shifts: 464
  - ¹⁵N chemical shifts: 112
- Completeness of assignments
  - Entity_assemble_ID: A
- 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 (%)
¹H chemical shifts	696	636	91.4
¹³C chemical shifts	511	464	90.8
¹⁵N chemical shifts	122	112	91.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	215	212	98.6
¹³C chemical shifts	214	207	96.7
¹⁵N chemical shifts	103	101	98.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	481	424	88.1
¹³C chemical shifts	297	257	86.5
¹⁵N chemical shifts	19	11	57.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	64	56	87.5
¹³C chemical shifts	64	56	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	49	35	71.4
¹³C chemical shifts	47	21	44.7
¹⁵N chemical shifts	2	2	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 98.1%
- Total number of restraints: 2464
- Weight of restraints: 1.0 (2464)
- Potential type of restraints: square-well-parabolic (2464)
- Range of distance target values: 1.26, 3.21 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 107, Sequence coverage: 60.7%
- Total number of restraints: 94
- Total number of restraints per polymer type: 94
- Weight of restraints: 1.0 (94)
- Potential type of restraints: square-well-parabolic (94)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, PSI-2, Structural Genomics, Target FR824D

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Found 1 Document (1.386 seconds)

BMRB: 18095

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. FR824D, : 1 : 2 : 106 entities Detail

Interaction partners 1. FR824D, : 8 interactors Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 4 contents Detail